diff --git a/notebooks/00_basic_usage/write_read_sidpy_dataset.ipynb b/notebooks/00_basic_usage/write_read_sidpy_dataset.ipynb index f15976e..af41b22 100644 --- a/notebooks/00_basic_usage/write_read_sidpy_dataset.ipynb +++ b/notebooks/00_basic_usage/write_read_sidpy_dataset.ipynb @@ -553,7 +553,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.6" + "version": "3.8.8" }, "toc": { "base_numbering": 1, @@ -571,4 +571,4 @@ }, "nbformat": 4, "nbformat_minor": 4 -} \ No newline at end of file +} diff --git a/notebooks/00_basic_usage/write_sidpy to_NeXus.ipynb b/notebooks/00_basic_usage/write_sidpy to_NeXus.ipynb new file mode 100644 index 0000000..219769a --- /dev/null +++ b/notebooks/00_basic_usage/write_sidpy to_NeXus.ipynb @@ -0,0 +1,2580 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "a28f140d", + "metadata": {}, + "source": [ + "https://manual.nexusformat.org/classes/base_classes/index.html#base-class-definitions" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "a8efb990", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Populating the interactive namespace from numpy and matplotlib\n" + ] + } + ], + "source": [ + "%pylab notebook\n", + "\n", + "import h5py\n", + "import numpy as np\n", + "\n", + "import sidpy\n", + "\n", + "import sys\n", + "sys.path.insert(0, '../../')\n", + "import datetime\n", + "import pyNSID" + ] + }, + { + "cell_type": "markdown", + "id": "d79abb5a", + "metadata": {}, + "source": [ + "## Make sidpy dataset" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "935ca0ff", + "metadata": {}, + "outputs": [], + "source": [ + "dataset = sidpy.Dataset.from_array(np.random.random([4, 5]), name='new')\n", + "\n", + "dataset.data_type = 'IMAGE'\n", + "dataset.units = 'nA'\n", + "dataset.quantity = 'Current'\n", + "dataset.title = 'random'\n", + "\n", + "dataset.set_dimension(0, sidpy.Dimension(np.arange(dataset.shape[0]), 'x',\n", + " units='nm', quantity='Length',\n", + " dimension_type='spatial'))\n", + "dataset.set_dimension(1, sidpy.Dimension(np.linspace(-2, 2, num=dataset.shape[1], endpoint=True), 'y', \n", + " units='nm', quantity='Length',\n", + " dimension_type='spatial'))\n" + ] + }, + { + "cell_type": "markdown", + "id": "5a20965d", + "metadata": {}, + "source": [ + "## Write pyNSID file normally" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "3b3aa6f6", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "../..\\pyNSID\\io\\hdf_utils.py:352: FutureWarning: validate_h5_dimension may be removed in a future version\n", + " warn('validate_h5_dimension may be removed in a future version',\n" + ] + } + ], + "source": [ + "file_name = \"test2.hf5\"\n", + "\n", + "h5_file = h5py.File(file_name, 'a')\n", + "\n", + "if 'Measurement_000' in h5_file:\n", + " h5_group = sidpy.hdf.prov_utils.create_indexed_group(h5_group, 'Measurement_')\n", + "else:\n", + " h5_group = h5_file.create_group('Measurement_000')\n", + "\n", + "if 'Channel_000' in h5_group:\n", + " h5_group = sidpy.hdf.prov_utils.create_indexed_group(h5_group, 'Channel_')\n", + "else:\n", + " h5_group = h5_group.create_group('Channel_000')\n", + "\n", + "dataset.h5_dataset = pyNSID.hdf_io.write_nsid_dataset(dataset, h5_group)\n" + ] + }, + { + "cell_type": "markdown", + "id": "287a1c7a", + "metadata": {}, + "source": [ + "## Make NeXus format compatible" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "5aac6f04", + "metadata": {}, + "outputs": [], + "source": [ + "def make_nexus_compatible(h5_dataset):\n", + " \n", + " time_stamp = \"T\".join( str( datetime.datetime.now() ).split() )\n", + " h5_file = h5_dataset.file\n", + " h5_group = h5_dataset.parent.parent\n", + " h5_file.attrs[u'default'] = h5_dataset.parent.parent.name\n", + "\n", + " # give the HDF5 root some more attributes\n", + "\n", + " h5_file.attrs[u'file_name'] = h5_file.filename\n", + " h5_file.attrs[u'file_time'] = time_stamp\n", + " h5_file.attrs[u'instrument'] = u'None'\n", + " h5_file.attrs[u'creator'] = u'pyNSID'\n", + " h5_file.attrs[u'NeXus_version'] = u'4.3.0'\n", + " h5_file.attrs[u'HDF5_Version'] = h5py.version.hdf5_version\n", + " h5_file.attrs[u'h5py_version'] = h5py.version.version\n", + "\n", + " h5_file.attrs[u'default'] = h5_group.name\n", + "\n", + " h5_group.attrs[u'NX_class'] = u'NXentry'\n", + " h5_group.attrs[u'default'] = h5_dataset.name.split('/')[-1]\n", + "\n", + " if 'title' in h5_group:\n", + " del h5_group['title']\n", + " h5_group.create_dataset(u'title', data=h5_dataset.name.split('/')[-1])\n", + " \n", + " nxdata = h5_dataset.parent\n", + "\n", + " nxdata.attrs[u'NX_class'] = u'NXdata'\n", + " nxdata.attrs[u'signal'] = h5_dataset.name.split('/')[-1] # Y axis of default plot\n", + "\n", + " axes = []\n", + " for dimension_label in h5_dataset.attrs['DIMENSION_LABELS']:\n", + " axes.append(dimension_label.decode('utf8'))\n", + " \n", + " nxdata.attrs[u'axes'] = axes # X axis of default plot\n", + " for i, axis in enumerate(axes):\n", + " nxdata.attrs[axes[i]+'_indices'] = [i,] \n", + " \n", + "# pyNSID.hdf_utils.make_nexus_compatible(dataset.h5_dataset)\n", + "make_nexus_compatible(dataset.h5_dataset)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "id": "872a63fa", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[b'x' b'y']\n", + "{'0': array([0., 1., 2., 3.]), '1': array([-2., -1., 0., 1., 2.])}\n" + ] + } + ], + "source": [ + "print(dataset.h5_dataset.attrs['DIMENSION_LABELS'])\n", + "print(dict(dataset.h5_dataset.parent['_axes'].attrs))" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "aa74c1c3", + "metadata": {}, + "outputs": [], + "source": [ + "h5_file.close()" + ] + }, + { + "cell_type": "markdown", + "id": "2d198bea", + "metadata": {}, + "source": [ + "## Read with nexusformat" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "id": "1a902f12", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "root:NXroot\n", + " @HDF5_Version = '1.10.4'\n", + " @NeXus_version = '4.3.0'\n", + " @creator = 'pyNSID'\n", + " @default = '/Measurement_000/Channel_000'\n", + " @file_name = 'test2.hf5'\n", + " @file_time = '2021-08-20T19:12:32.483537'\n", + " @h5py_version = '2.10.0'\n", + " @instrument = 'None'\n", + " Measurement_000:NXgroup\n", + " Channel_000:NXentry\n", + " @default = 'random'\n", + " random:NXdata\n", + " @axes = ['x', 'y']\n", + " @machine_id = 'DESKTOP-UM3713R'\n", + " @platform = 'Windows-10-10.0.19041-SP0'\n", + " @pyNSID_version = '0.0.2'\n", + " @sidpy_version = '0.0.5'\n", + " @signal = 'random'\n", + " @timestamp = '2021_08_20-18_59_19'\n", + " @x_indices = 0\n", + " @y_indices = 1\n", + " __dict__:NXgroup\n", + " @_axes-0 = [0. 1. 2. 3.]\n", + " @_axes-1 = [-2. -1. 0. 1. 2.]\n", + " @_data_type = 'IMAGE'\n", + " @_modality = 'generic'\n", + " @_quantity = 'Current'\n", + " @_source = 'generic'\n", + " @_title = 'random'\n", + " @_units = 'nA'\n", + " @a = [0. 1. 2. 3.]\n", + " @b = [0. 1. 2. 3. 4.]\n", + " @dim_0 = [0. 1. 2. 3.]\n", + " @dim_1 = [-2. -1. 0. 1. 2.]\n", + " @ndim = 2\n", + " @numblocks = [1 1]\n", + " @shape = [4 5]\n", + " @x = [0. 1. 2. 3.]\n", + " @y = [-2. -1. 0. 1. 2.]\n", + " _axes:NXgroup\n", + " @0 = [0. 1. 2. 3.]\n", + " @1 = [-2. -1. 0. 1. 2.]\n", + " random = float64(4x5)\n", + " @DIMENSION_LABELS = ['x', 'y']\n", + " @DIMENSION_LIST = ['', ', 0)\n", + " @dimension_type = 'SPATIAL'\n", + " @name = 'x'\n", + " @quantity = 'Length'\n", + " @units = 'nm'\n", + " y = float64(5)\n", + " @CLASS = 'DIMENSION_SCALE'\n", + " @NAME = 'y'\n", + " @REFERENCE_LIST = (, 1)\n", + " @dimension_type = 'SPATIAL'\n", + " @name = 'y'\n", + " @quantity = 'Length'\n", + " @units = 'nm'\n", + " title = 'random'\n" + ] + } + ], + "source": [ + "from nexusformat import nexus\n", + "nexus_dataset = nexus.nxload(file_name)\n", + "\n", + "print(nexus_dataset.tree)" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "id": "2ac36627", + "metadata": {}, + "outputs": [ + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "/* global mpl */\n", + "window.mpl = {};\n", + "\n", + "mpl.get_websocket_type = function () {\n", + " if (typeof WebSocket !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof MozWebSocket !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert(\n", + " 'Your browser does not have WebSocket support. ' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", + " 'Firefox 4 and 5 are also supported but you ' +\n", + " 'have to enable WebSockets in about:config.'\n", + " );\n", + " }\n", + "};\n", + "\n", + "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", + " this.id = figure_id;\n", + "\n", + " this.ws = websocket;\n", + "\n", + " this.supports_binary = this.ws.binaryType !== undefined;\n", + "\n", + " if (!this.supports_binary) {\n", + " var warnings = document.getElementById('mpl-warnings');\n", + " if (warnings) {\n", + " warnings.style.display = 'block';\n", + " warnings.textContent =\n", + " 'This browser does not support binary websocket messages. ' +\n", + " 'Performance may be slow.';\n", + " }\n", + " }\n", + "\n", + " this.imageObj = new Image();\n", + "\n", + " this.context = undefined;\n", + " this.message = undefined;\n", + " this.canvas = undefined;\n", + " this.rubberband_canvas = undefined;\n", + " this.rubberband_context = undefined;\n", + " this.format_dropdown = undefined;\n", + "\n", + " this.image_mode = 'full';\n", + "\n", + " this.root = document.createElement('div');\n", + " this.root.setAttribute('style', 'display: inline-block');\n", + " this._root_extra_style(this.root);\n", + "\n", + " parent_element.appendChild(this.root);\n", + "\n", + " this._init_header(this);\n", + " this._init_canvas(this);\n", + " this._init_toolbar(this);\n", + "\n", + " var fig = this;\n", + "\n", + " this.waiting = false;\n", + "\n", + " this.ws.onopen = function () {\n", + " fig.send_message('supports_binary', { value: fig.supports_binary });\n", + " fig.send_message('send_image_mode', {});\n", + " if (fig.ratio !== 1) {\n", + " fig.send_message('set_dpi_ratio', { dpi_ratio: fig.ratio });\n", + " }\n", + " fig.send_message('refresh', {});\n", + " };\n", + "\n", + " this.imageObj.onload = function () {\n", + " if (fig.image_mode === 'full') {\n", + " // Full images could contain transparency (where diff images\n", + " // almost always do), so we need to clear the canvas so that\n", + " // there is no ghosting.\n", + " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", + " }\n", + " fig.context.drawImage(fig.imageObj, 0, 0);\n", + " };\n", + "\n", + " this.imageObj.onunload = function () {\n", + " fig.ws.close();\n", + " };\n", + "\n", + " this.ws.onmessage = this._make_on_message_function(this);\n", + "\n", + " this.ondownload = ondownload;\n", + "};\n", + "\n", + "mpl.figure.prototype._init_header = function () {\n", + " var titlebar = document.createElement('div');\n", + " titlebar.classList =\n", + " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", + " var titletext = document.createElement('div');\n", + " titletext.classList = 'ui-dialog-title';\n", + " titletext.setAttribute(\n", + " 'style',\n", + " 'width: 100%; text-align: center; padding: 3px;'\n", + " );\n", + " titlebar.appendChild(titletext);\n", + " this.root.appendChild(titlebar);\n", + " this.header = titletext;\n", + "};\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", + "\n", + "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", + "\n", + "mpl.figure.prototype._init_canvas = function () {\n", + " var fig = this;\n", + "\n", + " var canvas_div = (this.canvas_div = document.createElement('div'));\n", + " canvas_div.setAttribute(\n", + " 'style',\n", + " 'border: 1px solid #ddd;' +\n", + " 'box-sizing: content-box;' +\n", + " 'clear: both;' +\n", + " 'min-height: 1px;' +\n", + " 'min-width: 1px;' +\n", + " 'outline: 0;' +\n", + " 'overflow: hidden;' +\n", + " 'position: relative;' +\n", + " 'resize: both;'\n", + " );\n", + "\n", + " function on_keyboard_event_closure(name) {\n", + " return function (event) {\n", + " return fig.key_event(event, name);\n", + " };\n", + " }\n", + "\n", + " canvas_div.addEventListener(\n", + " 'keydown',\n", + " on_keyboard_event_closure('key_press')\n", + " );\n", + " canvas_div.addEventListener(\n", + " 'keyup',\n", + " on_keyboard_event_closure('key_release')\n", + " );\n", + "\n", + " this._canvas_extra_style(canvas_div);\n", + " this.root.appendChild(canvas_div);\n", + "\n", + " var canvas = (this.canvas = document.createElement('canvas'));\n", + " canvas.classList.add('mpl-canvas');\n", + " canvas.setAttribute('style', 'box-sizing: content-box;');\n", + "\n", + " this.context = canvas.getContext('2d');\n", + "\n", + " var backingStore =\n", + " this.context.backingStorePixelRatio ||\n", + " this.context.webkitBackingStorePixelRatio ||\n", + " this.context.mozBackingStorePixelRatio ||\n", + " this.context.msBackingStorePixelRatio ||\n", + " this.context.oBackingStorePixelRatio ||\n", + " this.context.backingStorePixelRatio ||\n", + " 1;\n", + "\n", + " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", + "\n", + " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", + " 'canvas'\n", + " ));\n", + " rubberband_canvas.setAttribute(\n", + " 'style',\n", + " 'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n", + " );\n", + "\n", + " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", + " if (this.ResizeObserver === undefined) {\n", + " if (window.ResizeObserver !== undefined) {\n", + " this.ResizeObserver = window.ResizeObserver;\n", + " } else {\n", + " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", + " this.ResizeObserver = obs.ResizeObserver;\n", + " }\n", + " }\n", + "\n", + " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", + " var nentries = entries.length;\n", + " for (var i = 0; i < nentries; i++) {\n", + " var entry = entries[i];\n", + " var width, height;\n", + " if (entry.contentBoxSize) {\n", + " if (entry.contentBoxSize instanceof Array) {\n", + " // Chrome 84 implements new version of spec.\n", + " width = entry.contentBoxSize[0].inlineSize;\n", + " height = entry.contentBoxSize[0].blockSize;\n", + " } else {\n", + " // Firefox implements old version of spec.\n", + " width = entry.contentBoxSize.inlineSize;\n", + " height = entry.contentBoxSize.blockSize;\n", + " }\n", + " } else {\n", + " // Chrome <84 implements even older version of spec.\n", + " width = entry.contentRect.width;\n", + " height = entry.contentRect.height;\n", + " }\n", + "\n", + " // Keep the size of the canvas and rubber band canvas in sync with\n", + " // the canvas container.\n", + " if (entry.devicePixelContentBoxSize) {\n", + " // Chrome 84 implements new version of spec.\n", + " canvas.setAttribute(\n", + " 'width',\n", + " entry.devicePixelContentBoxSize[0].inlineSize\n", + " );\n", + " canvas.setAttribute(\n", + " 'height',\n", + " entry.devicePixelContentBoxSize[0].blockSize\n", + " );\n", + " } else {\n", + " canvas.setAttribute('width', width * fig.ratio);\n", + " canvas.setAttribute('height', height * fig.ratio);\n", + " }\n", + " canvas.setAttribute(\n", + " 'style',\n", + " 'width: ' + width + 'px; height: ' + height + 'px;'\n", + " );\n", + "\n", + " rubberband_canvas.setAttribute('width', width);\n", + " rubberband_canvas.setAttribute('height', height);\n", + "\n", + " // And update the size in Python. 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rubberband_canvas.addEventListener(\n", + " 'mouseenter',\n", + " on_mouse_event_closure('figure_enter')\n", + " );\n", + " rubberband_canvas.addEventListener(\n", + " 'mouseleave',\n", + " on_mouse_event_closure('figure_leave')\n", + " );\n", + "\n", + " canvas_div.addEventListener('wheel', function (event) {\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " on_mouse_event_closure('scroll')(event);\n", + " });\n", + "\n", + " canvas_div.appendChild(canvas);\n", + " canvas_div.appendChild(rubberband_canvas);\n", + "\n", + " this.rubberband_context = rubberband_canvas.getContext('2d');\n", + " this.rubberband_context.strokeStyle = '#000000';\n", + "\n", + " this._resize_canvas = function (width, height, forward) {\n", + " if (forward) {\n", + " canvas_div.style.width = width + 'px';\n", + " canvas_div.style.height = height + 'px';\n", + " }\n", + " };\n", + "\n", + " // Disable right mouse context menu.\n", + " this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n", + " event.preventDefault();\n", + " return false;\n", + " });\n", + "\n", + " function set_focus() {\n", + " canvas.focus();\n", + " canvas_div.focus();\n", + " }\n", + "\n", + " window.setTimeout(set_focus, 100);\n", + "};\n", + "\n", + "mpl.figure.prototype._init_toolbar = function () {\n", + " var fig = this;\n", + "\n", + " var toolbar = document.createElement('div');\n", + " toolbar.classList = 'mpl-toolbar';\n", + " this.root.appendChild(toolbar);\n", + "\n", + " function on_click_closure(name) {\n", + " return function (_event) {\n", + " return fig.toolbar_button_onclick(name);\n", + " };\n", + " }\n", + "\n", + " function on_mouseover_closure(tooltip) {\n", + " return function (event) {\n", + " if (!event.currentTarget.disabled) {\n", + " return fig.toolbar_button_onmouseover(tooltip);\n", + " }\n", + " };\n", + " }\n", + "\n", + " fig.buttons = {};\n", + " var buttonGroup = document.createElement('div');\n", + " buttonGroup.classList = 'mpl-button-group';\n", + " for (var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " /* Instead of a spacer, we start a new button group. */\n", + " if (buttonGroup.hasChildNodes()) {\n", + " toolbar.appendChild(buttonGroup);\n", + " }\n", + " buttonGroup = document.createElement('div');\n", + " buttonGroup.classList = 'mpl-button-group';\n", + " continue;\n", + " }\n", + "\n", + " var button = (fig.buttons[name] = document.createElement('button'));\n", + " button.classList = 'mpl-widget';\n", + " button.setAttribute('role', 'button');\n", + " button.setAttribute('aria-disabled', 'false');\n", + " button.addEventListener('click', on_click_closure(method_name));\n", + " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", + "\n", + " var icon_img = document.createElement('img');\n", + " icon_img.src = '_images/' + image + '.png';\n", + " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", + " icon_img.alt = tooltip;\n", + " button.appendChild(icon_img);\n", + "\n", + " buttonGroup.appendChild(button);\n", + " }\n", + "\n", + " if (buttonGroup.hasChildNodes()) {\n", + " toolbar.appendChild(buttonGroup);\n", + " }\n", + "\n", + " var fmt_picker = document.createElement('select');\n", + " fmt_picker.classList = 'mpl-widget';\n", + " toolbar.appendChild(fmt_picker);\n", + " this.format_dropdown = fmt_picker;\n", + "\n", + " for (var ind in mpl.extensions) {\n", + " var fmt = mpl.extensions[ind];\n", + " var option = document.createElement('option');\n", + " option.selected = fmt === mpl.default_extension;\n", + " option.innerHTML = fmt;\n", + " fmt_picker.appendChild(option);\n", + " }\n", + "\n", + " var status_bar = document.createElement('span');\n", + " status_bar.classList = 'mpl-message';\n", + " toolbar.appendChild(status_bar);\n", + " this.message = status_bar;\n", + "};\n", + "\n", + "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", + " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", + " // which will in turn request a refresh of the image.\n", + " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", + "};\n", + "\n", + "mpl.figure.prototype.send_message = function (type, properties) {\n", + " properties['type'] = type;\n", + " properties['figure_id'] = this.id;\n", + " this.ws.send(JSON.stringify(properties));\n", + "};\n", + "\n", + "mpl.figure.prototype.send_draw_message = function () {\n", + " if (!this.waiting) {\n", + " this.waiting = true;\n", + " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", + " var format_dropdown = fig.format_dropdown;\n", + " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", + " fig.ondownload(fig, format);\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", + " var size = msg['size'];\n", + " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", + " fig._resize_canvas(size[0], size[1], msg['forward']);\n", + " fig.send_message('refresh', {});\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", + " var x0 = msg['x0'] / fig.ratio;\n", + " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", + " var x1 = msg['x1'] / fig.ratio;\n", + " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", + " x0 = Math.floor(x0) + 0.5;\n", + " y0 = Math.floor(y0) + 0.5;\n", + " x1 = Math.floor(x1) + 0.5;\n", + " y1 = Math.floor(y1) + 0.5;\n", + " var min_x = Math.min(x0, x1);\n", + " var min_y = Math.min(y0, y1);\n", + " var width = Math.abs(x1 - x0);\n", + " var height = Math.abs(y1 - y0);\n", + "\n", + " fig.rubberband_context.clearRect(\n", + " 0,\n", + " 0,\n", + " fig.canvas.width / fig.ratio,\n", + " fig.canvas.height / fig.ratio\n", + " );\n", + "\n", + " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", + " // Updates the figure title.\n", + " fig.header.textContent = msg['label'];\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", + " var cursor = msg['cursor'];\n", + " switch (cursor) {\n", + " case 0:\n", + " cursor = 'pointer';\n", + " break;\n", + " case 1:\n", + " cursor = 'default';\n", + " break;\n", + " case 2:\n", + " cursor = 'crosshair';\n", + " break;\n", + " case 3:\n", + " cursor = 'move';\n", + " break;\n", + " }\n", + " fig.rubberband_canvas.style.cursor = cursor;\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_message = function (fig, msg) {\n", + " fig.message.textContent = msg['message'];\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", + " // Request the server to send over a new figure.\n", + " fig.send_draw_message();\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", + " fig.image_mode = msg['mode'];\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", + " for (var key in msg) {\n", + " if (!(key in fig.buttons)) {\n", + " continue;\n", + " }\n", + " fig.buttons[key].disabled = !msg[key];\n", + " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", + " if (msg['mode'] === 'PAN') {\n", + " fig.buttons['Pan'].classList.add('active');\n", + " fig.buttons['Zoom'].classList.remove('active');\n", + " } else if (msg['mode'] === 'ZOOM') {\n", + " fig.buttons['Pan'].classList.remove('active');\n", + " fig.buttons['Zoom'].classList.add('active');\n", + " } else {\n", + " fig.buttons['Pan'].classList.remove('active');\n", + " fig.buttons['Zoom'].classList.remove('active');\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.updated_canvas_event = function () {\n", + " // Called whenever the canvas gets updated.\n", + " this.send_message('ack', {});\n", + "};\n", + "\n", + "// A function to construct a web socket function for onmessage handling.\n", + "// Called in the figure constructor.\n", + "mpl.figure.prototype._make_on_message_function = function (fig) {\n", + " return function socket_on_message(evt) {\n", + " if (evt.data instanceof Blob) {\n", + " /* FIXME: We get \"Resource interpreted as Image but\n", + " * transferred with MIME type text/plain:\" errors on\n", + " * Chrome. But how to set the MIME type? It doesn't seem\n", + " * to be part of the websocket stream */\n", + " evt.data.type = 'image/png';\n", + "\n", + " /* Free the memory for the previous frames */\n", + " if (fig.imageObj.src) {\n", + " (window.URL || window.webkitURL).revokeObjectURL(\n", + " fig.imageObj.src\n", + " );\n", + " }\n", + "\n", + " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", + " evt.data\n", + " );\n", + " fig.updated_canvas_event();\n", + " fig.waiting = false;\n", + " return;\n", + " } else if (\n", + " typeof evt.data === 'string' &&\n", + " evt.data.slice(0, 21) === 'data:image/png;base64'\n", + " ) {\n", + " fig.imageObj.src = evt.data;\n", + " fig.updated_canvas_event();\n", + " fig.waiting = false;\n", + " return;\n", + " }\n", + "\n", + " var msg = JSON.parse(evt.data);\n", + " var msg_type = msg['type'];\n", + "\n", + " // Call the \"handle_{type}\" callback, which takes\n", + " // the figure and JSON message as its only arguments.\n", + " try {\n", + " var callback = fig['handle_' + msg_type];\n", + " } catch (e) {\n", + " console.log(\n", + " \"No handler for the '\" + msg_type + \"' message type: \",\n", + " msg\n", + " );\n", + " return;\n", + " }\n", + "\n", + " if (callback) {\n", + " try {\n", + " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", + " callback(fig, msg);\n", + " } catch (e) {\n", + " console.log(\n", + " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", + " e,\n", + " e.stack,\n", + " msg\n", + " );\n", + " }\n", + " }\n", + " };\n", + "};\n", + "\n", + "// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n", + "mpl.findpos = function (e) {\n", + " //this section is from http://www.quirksmode.org/js/events_properties.html\n", + " var targ;\n", + " if (!e) {\n", + " e = window.event;\n", + " }\n", + " if (e.target) {\n", + " targ = e.target;\n", + " } else if (e.srcElement) {\n", + " targ = e.srcElement;\n", + " }\n", + " if (targ.nodeType === 3) {\n", + " // defeat Safari bug\n", + " targ = targ.parentNode;\n", + " }\n", + "\n", + " // pageX,Y are the mouse positions relative to the document\n", + " var boundingRect = targ.getBoundingClientRect();\n", + " var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n", + " var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n", + "\n", + " return { x: x, y: y };\n", + "};\n", + "\n", + "/*\n", + " * return a copy of an object with only non-object keys\n", + " * we need this to avoid circular references\n", + " * http://stackoverflow.com/a/24161582/3208463\n", + " */\n", + "function simpleKeys(original) {\n", + " return Object.keys(original).reduce(function (obj, key) {\n", + " if (typeof original[key] !== 'object') {\n", + " obj[key] = original[key];\n", + " }\n", + " return obj;\n", + " }, {});\n", + "}\n", + "\n", + "mpl.figure.prototype.mouse_event = function (event, name) {\n", + " var canvas_pos = mpl.findpos(event);\n", + "\n", + " if (name === 'button_press') {\n", + " this.canvas.focus();\n", + " this.canvas_div.focus();\n", + " }\n", + "\n", + " var x = canvas_pos.x * this.ratio;\n", + " var y = canvas_pos.y * this.ratio;\n", + "\n", + " this.send_message(name, {\n", + " x: x,\n", + " y: y,\n", + " button: event.button,\n", + " step: event.step,\n", + " guiEvent: simpleKeys(event),\n", + " });\n", + "\n", + " /* This prevents the web browser from automatically changing to\n", + " * the text insertion cursor when the button is pressed. We want\n", + " * to control all of the cursor setting manually through the\n", + " * 'cursor' event from matplotlib */\n", + " event.preventDefault();\n", + " return false;\n", + "};\n", + "\n", + "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", + " // Handle any extra behaviour associated with a key event\n", + "};\n", + "\n", + "mpl.figure.prototype.key_event = function (event, name) {\n", + " // Prevent repeat events\n", + " if (name === 'key_press') {\n", + " if (event.which === this._key) {\n", + " return;\n", + " } else {\n", + " this._key = event.which;\n", + " }\n", + " }\n", + " if (name === 'key_release') {\n", + " this._key = null;\n", + " }\n", + "\n", + " var value = '';\n", + " if (event.ctrlKey && event.which !== 17) {\n", + " value += 'ctrl+';\n", + " }\n", + " if (event.altKey && event.which !== 18) {\n", + " value += 'alt+';\n", + " }\n", + " if (event.shiftKey && event.which !== 16) {\n", + " value += 'shift+';\n", + " }\n", + "\n", + " value += 'k';\n", + " value += event.which.toString();\n", + "\n", + " this._key_event_extra(event, name);\n", + "\n", + " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", + " return false;\n", + "};\n", + "\n", + "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", + " if (name === 'download') {\n", + " this.handle_save(this, null);\n", + " } else {\n", + " this.send_message('toolbar_button', { name: name });\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", + " this.message.textContent = tooltip;\n", + "};\n", + "\n", + "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", + "// prettier-ignore\n", + "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", + "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n", + "\n", + "mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n", + "\n", + "mpl.default_extension = \"png\";/* global mpl */\n", + "\n", + "var comm_websocket_adapter = function (comm) {\n", + " // Create a \"websocket\"-like object which calls the given IPython comm\n", + " // object with the appropriate methods. Currently this is a non binary\n", + " // socket, so there is still some room for performance tuning.\n", + " var ws = {};\n", + "\n", + " ws.close = function () {\n", + " comm.close();\n", + " };\n", + " ws.send = function (m) {\n", + " //console.log('sending', m);\n", + " comm.send(m);\n", + " };\n", + " // Register the callback with on_msg.\n", + " comm.on_msg(function (msg) {\n", + " //console.log('receiving', msg['content']['data'], msg);\n", + " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", + " ws.onmessage(msg['content']['data']);\n", + " });\n", + " return ws;\n", + "};\n", + "\n", + "mpl.mpl_figure_comm = function (comm, msg) {\n", + " // This is the function which gets called when the mpl process\n", + " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", + "\n", + " var id = msg.content.data.id;\n", + " // Get hold of the div created by the display call when the Comm\n", + " // socket was opened in Python.\n", + " var element = document.getElementById(id);\n", + " var ws_proxy = comm_websocket_adapter(comm);\n", + "\n", + " function ondownload(figure, _format) {\n", + " window.open(figure.canvas.toDataURL());\n", + " }\n", + "\n", + " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", + "\n", + " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", + " // web socket which is closed, not our websocket->open comm proxy.\n", + " ws_proxy.onopen();\n", + "\n", + " fig.parent_element = element;\n", + " fig.cell_info = mpl.find_output_cell(\"
\");\n", + " if (!fig.cell_info) {\n", + " console.error('Failed to find cell for figure', id, fig);\n", + " return;\n", + " }\n", + " fig.cell_info[0].output_area.element.on(\n", + " 'cleared',\n", + " { fig: fig },\n", + " fig._remove_fig_handler\n", + " );\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_close = function (fig, msg) {\n", + " var width = fig.canvas.width / fig.ratio;\n", + " fig.cell_info[0].output_area.element.off(\n", + " 'cleared',\n", + " fig._remove_fig_handler\n", + " );\n", + " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", + "\n", + " // Update the output cell to use the data from the current canvas.\n", + " fig.push_to_output();\n", + " var dataURL = fig.canvas.toDataURL();\n", + " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", + " // the notebook keyboard shortcuts fail.\n", + " IPython.keyboard_manager.enable();\n", + " fig.parent_element.innerHTML =\n", + " '';\n", + " fig.close_ws(fig, msg);\n", + "};\n", + "\n", + "mpl.figure.prototype.close_ws = function (fig, msg) {\n", + " fig.send_message('closing', msg);\n", + " // fig.ws.close()\n", + "};\n", + "\n", + "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", + " // Turn the data on the canvas into data in the output cell.\n", + " var width = this.canvas.width / this.ratio;\n", + " var dataURL = this.canvas.toDataURL();\n", + " this.cell_info[1]['text/html'] =\n", + " '';\n", + "};\n", + "\n", + "mpl.figure.prototype.updated_canvas_event = function () {\n", + " // Tell IPython that the notebook contents must change.\n", + " IPython.notebook.set_dirty(true);\n", + " this.send_message('ack', {});\n", + " var fig = this;\n", + " // Wait a second, then push the new image to the DOM so\n", + " // that it is saved nicely (might be nice to debounce this).\n", + " setTimeout(function () {\n", + " fig.push_to_output();\n", + " }, 1000);\n", + "};\n", + "\n", + "mpl.figure.prototype._init_toolbar = function () {\n", + " var fig = this;\n", + "\n", + " var toolbar = document.createElement('div');\n", + " toolbar.classList = 'btn-toolbar';\n", + " this.root.appendChild(toolbar);\n", + "\n", + " function on_click_closure(name) {\n", + " return function (_event) {\n", + " return fig.toolbar_button_onclick(name);\n", + " };\n", + " }\n", + "\n", + " function on_mouseover_closure(tooltip) {\n", + " return function (event) {\n", + " if (!event.currentTarget.disabled) {\n", + " return fig.toolbar_button_onmouseover(tooltip);\n", + " }\n", + " };\n", + " }\n", + "\n", + " fig.buttons = {};\n", + " var buttonGroup = document.createElement('div');\n", + " buttonGroup.classList = 'btn-group';\n", + " var button;\n", + " for (var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " /* Instead of a spacer, we start a new button group. */\n", + " if (buttonGroup.hasChildNodes()) {\n", + " toolbar.appendChild(buttonGroup);\n", + " }\n", + " buttonGroup = document.createElement('div');\n", + " buttonGroup.classList = 'btn-group';\n", + " continue;\n", + " }\n", + "\n", + " button = fig.buttons[name] = document.createElement('button');\n", + " button.classList = 'btn btn-default';\n", + " button.href = '#';\n", + " button.title = name;\n", + " button.innerHTML = '';\n", + " button.addEventListener('click', on_click_closure(method_name));\n", + " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", + " buttonGroup.appendChild(button);\n", + " }\n", + "\n", + " if (buttonGroup.hasChildNodes()) {\n", + " toolbar.appendChild(buttonGroup);\n", + " }\n", + "\n", + " // Add the status bar.\n", + " var status_bar = document.createElement('span');\n", + " status_bar.classList = 'mpl-message pull-right';\n", + " toolbar.appendChild(status_bar);\n", + " this.message = status_bar;\n", + "\n", + " // Add the close button to the window.\n", + " var buttongrp = document.createElement('div');\n", + " buttongrp.classList = 'btn-group inline pull-right';\n", + " button = document.createElement('button');\n", + " button.classList = 'btn btn-mini btn-primary';\n", + " button.href = '#';\n", + " button.title = 'Stop Interaction';\n", + " button.innerHTML = '';\n", + " button.addEventListener('click', function (_evt) {\n", + " fig.handle_close(fig, {});\n", + " });\n", + " button.addEventListener(\n", + " 'mouseover',\n", + " on_mouseover_closure('Stop Interaction')\n", + " );\n", + " buttongrp.appendChild(button);\n", + " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", + " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", + "};\n", + "\n", + "mpl.figure.prototype._remove_fig_handler = function (event) {\n", + " var fig = event.data.fig;\n", + " if (event.target !== this) {\n", + " // Ignore bubbled events from children.\n", + " return;\n", + " }\n", + " fig.close_ws(fig, {});\n", + "};\n", + "\n", + "mpl.figure.prototype._root_extra_style = function (el) {\n", + " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", + "};\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function (el) {\n", + " // this is important to make the div 'focusable\n", + " el.setAttribute('tabindex', 0);\n", + " // reach out to IPython and tell the keyboard manager to turn it's self\n", + " // off when our div gets focus\n", + "\n", + " // location in version 3\n", + " if (IPython.notebook.keyboard_manager) {\n", + " IPython.notebook.keyboard_manager.register_events(el);\n", + " } else {\n", + " // location in version 2\n", + " IPython.keyboard_manager.register_events(el);\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", + " var manager = IPython.notebook.keyboard_manager;\n", + " if (!manager) {\n", + " manager = IPython.keyboard_manager;\n", + " }\n", + "\n", + " // Check for shift+enter\n", + " if (event.shiftKey && event.which === 13) {\n", + " this.canvas_div.blur();\n", + " // select the cell after this one\n", + " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", + " IPython.notebook.select(index + 1);\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", + " fig.ondownload(fig, null);\n", + "};\n", + "\n", + "mpl.find_output_cell = function (html_output) {\n", + " // Return the cell and output element which can be found *uniquely* in the notebook.\n", + " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", + " // IPython event is triggered only after the cells have been serialised, which for\n", + " // our purposes (turning an active figure into a static one), is too late.\n", + " var cells = IPython.notebook.get_cells();\n", + " var ncells = cells.length;\n", + " for (var i = 0; i < ncells; i++) {\n", + " var cell = cells[i];\n", + " if (cell.cell_type === 'code') {\n", + " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", + " var data = cell.output_area.outputs[j];\n", + " if (data.data) {\n", + " // IPython >= 3 moved mimebundle to data attribute of output\n", + " data = data.data;\n", + " }\n", + " if (data['text/html'] === html_output) {\n", + " return [cell, data, j];\n", + " }\n", + " }\n", + " }\n", + " }\n", + "};\n", + "\n", + "// Register the function which deals with the matplotlib target/channel.\n", + "// The kernel may be null if the page has been refreshed.\n", + "if (IPython.notebook.kernel !== null) {\n", + " IPython.notebook.kernel.comm_manager.register_target(\n", + " 'matplotlib',\n", + " mpl.mpl_figure_comm\n", + " );\n", + "}\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "nexus_dataset.plot()" + ] + }, + { + "cell_type": "code", + "execution_count": 71, + "id": "c74e60dc", + "metadata": {}, + "outputs": [ + { + "ename": "NeXusError", + "evalue": "Invalid index", + "output_type": "error", + "traceback": [ + "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[1;31mNeXusError\u001b[0m Traceback (most recent call last)", + "\u001b[1;32m\u001b[0m in \u001b[0;36m\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0ma\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0ma\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mdefault\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[1;32m~\\anaconda3\\lib\\site-packages\\nexusformat\\nexus\\tree.py\u001b[0m in \u001b[0;36m__getitem__\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m 4327\u001b[0m \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mentries\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4328\u001b[0m \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 4329\u001b[1;33m \u001b[1;32mraise\u001b[0m \u001b[0mNeXusError\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"Invalid index\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m 4330\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m 4331\u001b[0m \u001b[1;32mdef\u001b[0m \u001b[0m__setitem__\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n", + "\u001b[1;31mNeXusError\u001b[0m: Invalid index" + ] + } + ], + "source": [ + "a[a.default]" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "id": "e6cbc2b5", + "metadata": {}, + "outputs": [], + "source": [ + "root = h5py.File('NXarpes.h5', 'w')\n", + "\n", + "# Create the GROUPS \n", + " \n", + "root.create_group('entry')\n", + "root['/entry'].attrs['NX_class'] = 'NXentry'\n", + "root['/entry'].attrs['EX_required'] = 'true'" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "id": "f74dada6", + "metadata": {}, + "outputs": [], + "source": [ + "# Create the FIELDS \n", + " \n", + "root['/entry'].create_dataset(name='title', data='SAMPLE-CHAR-DATA', maxshape=None)\n", + "root['/entry/title'].attrs['type'] = 'NX_CHAR'\n", + "root['/entry/title'].attrs['EX_required'] = 'true'" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "id": "aa34c240", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/\n", + "├ entry\n", + " -----\n", + " ├ title\n" + ] + } + ], + "source": [ + "sidpy.hdf.hdf_utils.print_tree(root)" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "b51bd121", + "metadata": {}, + "outputs": [], + "source": [ + "def find_NXgroup(h5_group):\n", + " \"\"\"\n", + " Uses visit() to find all groups with NX_class attribute\n", + "\n", + " Parameters\n", + " ----------\n", + " h5_group : :class:`h5py.Group`\n", + " Group to search within for the Dataset\n", + "\n", + " Returns\n", + " -------\n", + " groups : list\n", + " List of [object] corresponding to groups with attribute NX_class.\n", + "\n", + " \"\"\"\n", + " if not isinstance(h5_group, (h5py.File, h5py.Group)):\n", + " raise TypeError('h5_group should be a h5py.File or h5py.Group object')\n", + "\n", + " # print 'Finding all instances of', ds_name\n", + " groups = []\n", + "\n", + " def __find_name(name, obj):\n", + " if isinstance(obj, h5py.Group):\n", + " found_nexus_group = False\n", + " for key in dict(obj.attrs).keys():\n", + " if 'NX_class' in key: \n", + " found_nexus_group = True\n", + " if found_nexus_group:\n", + " groups.append(obj)\n", + " return\n", + "\n", + " h5_group.visititems(__find_name)\n", + "\n", + " return groups\n", + "\n", + "def find_nexus_class(groups, key):\n", + " nexus_class = None\n", + " for group in groups:\n", + " if dict(group.attrs)['NX_class'].decode('UTF-8') == key:\n", + " nexus_class = group\n", + " \n", + " return nexus_class\n", + "\n", + " " + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "id": "ae3aeaca", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "'2021-08-20T16:14:43.596847'" + ] + }, + "execution_count": 34, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "timestamp = \"T\".join(str( datetime.datetime.now() ).split())\n", + "timestamp" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "id": "acf507dc", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "[56.9965 57.009 57.0185 57.028 57.037 57.047 57.057 57.0675 57.0785\n", + " 57.0905 57.095 ]\n", + "{'spec_name': b'eta'}\n", + "[90.9 90.9105 90.921 90.9305 90.9405 90.951 90.961 90.9705 90.981\n", + " 90.991 91. ]\n", + "{'spec_name': b'chi'}\n", + "/S22/data\n", + "[0]\n", + "{'NX_class': b'NXdata', 'axes': array([b'eta', b'chi'], dtype='|S3'), 'chi_indices': array([0]), 'description': b'SPEC scan data', 'eta_indices': array([0]), 'signal': b'I0'}\n" + ] + }, + { + "data": { + "application/javascript": [ + "/* Put everything inside the global mpl namespace */\n", + "/* global mpl */\n", + "window.mpl = {};\n", + "\n", + "mpl.get_websocket_type = function () {\n", + " if (typeof WebSocket !== 'undefined') {\n", + " return WebSocket;\n", + " } else if (typeof MozWebSocket !== 'undefined') {\n", + " return MozWebSocket;\n", + " } else {\n", + " alert(\n", + " 'Your browser does not have WebSocket support. ' +\n", + " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", + " 'Firefox 4 and 5 are also supported but you ' +\n", + " 'have to enable WebSockets in about:config.'\n", + " );\n", + " }\n", + "};\n", + "\n", + "mpl.figure = function (figure_id, websocket, ondownload, parent_element) {\n", + " this.id = figure_id;\n", + "\n", + " this.ws = websocket;\n", + "\n", + " this.supports_binary = this.ws.binaryType !== undefined;\n", + "\n", + " if (!this.supports_binary) {\n", + " var warnings = document.getElementById('mpl-warnings');\n", + " if (warnings) {\n", + " warnings.style.display = 'block';\n", + " warnings.textContent =\n", + " 'This browser does not support binary websocket messages. ' +\n", + " 'Performance may be slow.';\n", + " }\n", + " }\n", + "\n", + " this.imageObj = new Image();\n", + "\n", + " this.context = undefined;\n", + " this.message = undefined;\n", + " this.canvas = undefined;\n", + " this.rubberband_canvas = undefined;\n", + " this.rubberband_context = undefined;\n", + " this.format_dropdown = undefined;\n", + "\n", + " this.image_mode = 'full';\n", + "\n", + " this.root = document.createElement('div');\n", + " this.root.setAttribute('style', 'display: inline-block');\n", + " this._root_extra_style(this.root);\n", + "\n", + " parent_element.appendChild(this.root);\n", + "\n", + " this._init_header(this);\n", + " this._init_canvas(this);\n", + " this._init_toolbar(this);\n", + "\n", + " var fig = this;\n", + "\n", + " this.waiting = false;\n", + "\n", + " this.ws.onopen = function () {\n", + " fig.send_message('supports_binary', { value: fig.supports_binary });\n", + " fig.send_message('send_image_mode', {});\n", + " if (fig.ratio !== 1) {\n", + " fig.send_message('set_dpi_ratio', { dpi_ratio: fig.ratio });\n", + " }\n", + " fig.send_message('refresh', {});\n", + " };\n", + "\n", + " this.imageObj.onload = function () {\n", + " if (fig.image_mode === 'full') {\n", + " // Full images could contain transparency (where diff images\n", + " // almost always do), so we need to clear the canvas so that\n", + " // there is no ghosting.\n", + " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", + " }\n", + " fig.context.drawImage(fig.imageObj, 0, 0);\n", + " };\n", + "\n", + " this.imageObj.onunload = function () {\n", + " fig.ws.close();\n", + " };\n", + "\n", + " this.ws.onmessage = this._make_on_message_function(this);\n", + "\n", + " this.ondownload = ondownload;\n", + "};\n", + "\n", + "mpl.figure.prototype._init_header = function () {\n", + " var titlebar = document.createElement('div');\n", + " titlebar.classList =\n", + " 'ui-dialog-titlebar ui-widget-header ui-corner-all ui-helper-clearfix';\n", + " var titletext = document.createElement('div');\n", + " titletext.classList = 'ui-dialog-title';\n", + " titletext.setAttribute(\n", + " 'style',\n", + " 'width: 100%; text-align: center; padding: 3px;'\n", + " );\n", + " titlebar.appendChild(titletext);\n", + " this.root.appendChild(titlebar);\n", + " this.header = titletext;\n", + "};\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function (_canvas_div) {};\n", + "\n", + "mpl.figure.prototype._root_extra_style = function (_canvas_div) {};\n", + "\n", + "mpl.figure.prototype._init_canvas = function () {\n", + " var fig = this;\n", + "\n", + " var canvas_div = (this.canvas_div = document.createElement('div'));\n", + " canvas_div.setAttribute(\n", + " 'style',\n", + " 'border: 1px solid #ddd;' +\n", + " 'box-sizing: content-box;' +\n", + " 'clear: both;' +\n", + " 'min-height: 1px;' +\n", + " 'min-width: 1px;' +\n", + " 'outline: 0;' +\n", + " 'overflow: hidden;' +\n", + " 'position: relative;' +\n", + " 'resize: both;'\n", + " );\n", + "\n", + " function on_keyboard_event_closure(name) {\n", + " return function (event) {\n", + " return fig.key_event(event, name);\n", + " };\n", + " }\n", + "\n", + " canvas_div.addEventListener(\n", + " 'keydown',\n", + " on_keyboard_event_closure('key_press')\n", + " );\n", + " canvas_div.addEventListener(\n", + " 'keyup',\n", + " on_keyboard_event_closure('key_release')\n", + " );\n", + "\n", + " this._canvas_extra_style(canvas_div);\n", + " this.root.appendChild(canvas_div);\n", + "\n", + " var canvas = (this.canvas = document.createElement('canvas'));\n", + " canvas.classList.add('mpl-canvas');\n", + " canvas.setAttribute('style', 'box-sizing: content-box;');\n", + "\n", + " this.context = canvas.getContext('2d');\n", + "\n", + " var backingStore =\n", + " this.context.backingStorePixelRatio ||\n", + " this.context.webkitBackingStorePixelRatio ||\n", + " this.context.mozBackingStorePixelRatio ||\n", + " this.context.msBackingStorePixelRatio ||\n", + " this.context.oBackingStorePixelRatio ||\n", + " this.context.backingStorePixelRatio ||\n", + " 1;\n", + "\n", + " this.ratio = (window.devicePixelRatio || 1) / backingStore;\n", + "\n", + " var rubberband_canvas = (this.rubberband_canvas = document.createElement(\n", + " 'canvas'\n", + " ));\n", + " rubberband_canvas.setAttribute(\n", + " 'style',\n", + " 'box-sizing: content-box; position: absolute; left: 0; top: 0; z-index: 1;'\n", + " );\n", + "\n", + " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", + " if (this.ResizeObserver === undefined) {\n", + " if (window.ResizeObserver !== undefined) {\n", + " this.ResizeObserver = window.ResizeObserver;\n", + " } else {\n", + " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", + " this.ResizeObserver = obs.ResizeObserver;\n", + " }\n", + " }\n", + "\n", + " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", + " var nentries = entries.length;\n", + " for (var i = 0; i < nentries; i++) {\n", + " var entry = entries[i];\n", + " var width, height;\n", + " if (entry.contentBoxSize) {\n", + " if (entry.contentBoxSize instanceof Array) {\n", + " // Chrome 84 implements new version of spec.\n", + " width = entry.contentBoxSize[0].inlineSize;\n", + " height = entry.contentBoxSize[0].blockSize;\n", + " } else {\n", + " // Firefox implements old version of spec.\n", + " width = entry.contentBoxSize.inlineSize;\n", + " height = entry.contentBoxSize.blockSize;\n", + " }\n", + " } else {\n", + " // Chrome <84 implements even older version of spec.\n", + " width = entry.contentRect.width;\n", + " height = entry.contentRect.height;\n", + " }\n", + "\n", + " // Keep the size of the canvas and rubber band canvas in sync with\n", + " // the canvas container.\n", + " if (entry.devicePixelContentBoxSize) {\n", + " // Chrome 84 implements new version of spec.\n", + " canvas.setAttribute(\n", + " 'width',\n", + " entry.devicePixelContentBoxSize[0].inlineSize\n", + " );\n", + " canvas.setAttribute(\n", + " 'height',\n", + " entry.devicePixelContentBoxSize[0].blockSize\n", + " );\n", + " } else {\n", + " canvas.setAttribute('width', width * fig.ratio);\n", + " canvas.setAttribute('height', height * fig.ratio);\n", + " }\n", + " canvas.setAttribute(\n", + " 'style',\n", + " 'width: ' + width + 'px; height: ' + height + 'px;'\n", + " );\n", + "\n", + " rubberband_canvas.setAttribute('width', width);\n", + " rubberband_canvas.setAttribute('height', height);\n", + "\n", + " // And update the size in Python. We ignore the initial 0/0 size\n", + " // that occurs as the element is placed into the DOM, which should\n", + " // otherwise not happen due to the minimum size styling.\n", + " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", + " fig.request_resize(width, height);\n", + " }\n", + " }\n", + " });\n", + " this.resizeObserverInstance.observe(canvas_div);\n", + "\n", + " function on_mouse_event_closure(name) {\n", + " return function (event) {\n", + " return fig.mouse_event(event, name);\n", + " };\n", + " }\n", + "\n", + " rubberband_canvas.addEventListener(\n", + " 'mousedown',\n", + " on_mouse_event_closure('button_press')\n", + " );\n", + " rubberband_canvas.addEventListener(\n", + " 'mouseup',\n", + " on_mouse_event_closure('button_release')\n", + " );\n", + " // Throttle sequential mouse events to 1 every 20ms.\n", + " rubberband_canvas.addEventListener(\n", + " 'mousemove',\n", + " on_mouse_event_closure('motion_notify')\n", + " );\n", + "\n", + " rubberband_canvas.addEventListener(\n", + " 'mouseenter',\n", + " on_mouse_event_closure('figure_enter')\n", + " );\n", + " rubberband_canvas.addEventListener(\n", + " 'mouseleave',\n", + " on_mouse_event_closure('figure_leave')\n", + " );\n", + "\n", + " canvas_div.addEventListener('wheel', function (event) {\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " on_mouse_event_closure('scroll')(event);\n", + " });\n", + "\n", + " canvas_div.appendChild(canvas);\n", + " canvas_div.appendChild(rubberband_canvas);\n", + "\n", + " this.rubberband_context = rubberband_canvas.getContext('2d');\n", + " this.rubberband_context.strokeStyle = '#000000';\n", + "\n", + " this._resize_canvas = function (width, height, forward) {\n", + " if (forward) {\n", + " canvas_div.style.width = width + 'px';\n", + " canvas_div.style.height = height + 'px';\n", + " }\n", + " };\n", + "\n", + " // Disable right mouse context menu.\n", + " this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n", + " event.preventDefault();\n", + " return false;\n", + " });\n", + "\n", + " function set_focus() {\n", + " canvas.focus();\n", + " canvas_div.focus();\n", + " }\n", + "\n", + " window.setTimeout(set_focus, 100);\n", + "};\n", + "\n", + "mpl.figure.prototype._init_toolbar = function () {\n", + " var fig = this;\n", + "\n", + " var toolbar = document.createElement('div');\n", + " toolbar.classList = 'mpl-toolbar';\n", + " this.root.appendChild(toolbar);\n", + "\n", + " function on_click_closure(name) {\n", + " return function (_event) {\n", + " return fig.toolbar_button_onclick(name);\n", + " };\n", + " }\n", + "\n", + " function on_mouseover_closure(tooltip) {\n", + " return function (event) {\n", + " if (!event.currentTarget.disabled) {\n", + " return fig.toolbar_button_onmouseover(tooltip);\n", + " }\n", + " };\n", + " }\n", + "\n", + " fig.buttons = {};\n", + " var buttonGroup = document.createElement('div');\n", + " buttonGroup.classList = 'mpl-button-group';\n", + " for (var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " /* Instead of a spacer, we start a new button group. */\n", + " if (buttonGroup.hasChildNodes()) {\n", + " toolbar.appendChild(buttonGroup);\n", + " }\n", + " buttonGroup = document.createElement('div');\n", + " buttonGroup.classList = 'mpl-button-group';\n", + " continue;\n", + " }\n", + "\n", + " var button = (fig.buttons[name] = document.createElement('button'));\n", + " button.classList = 'mpl-widget';\n", + " button.setAttribute('role', 'button');\n", + " button.setAttribute('aria-disabled', 'false');\n", + " button.addEventListener('click', on_click_closure(method_name));\n", + " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", + "\n", + " var icon_img = document.createElement('img');\n", + " icon_img.src = '_images/' + image + '.png';\n", + " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", + " icon_img.alt = tooltip;\n", + " button.appendChild(icon_img);\n", + "\n", + " buttonGroup.appendChild(button);\n", + " }\n", + "\n", + " if (buttonGroup.hasChildNodes()) {\n", + " toolbar.appendChild(buttonGroup);\n", + " }\n", + "\n", + " var fmt_picker = document.createElement('select');\n", + " fmt_picker.classList = 'mpl-widget';\n", + " toolbar.appendChild(fmt_picker);\n", + " this.format_dropdown = fmt_picker;\n", + "\n", + " for (var ind in mpl.extensions) {\n", + " var fmt = mpl.extensions[ind];\n", + " var option = document.createElement('option');\n", + " option.selected = fmt === mpl.default_extension;\n", + " option.innerHTML = fmt;\n", + " fmt_picker.appendChild(option);\n", + " }\n", + "\n", + " var status_bar = document.createElement('span');\n", + " status_bar.classList = 'mpl-message';\n", + " toolbar.appendChild(status_bar);\n", + " this.message = status_bar;\n", + "};\n", + "\n", + "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", + " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", + " // which will in turn request a refresh of the image.\n", + " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", + "};\n", + "\n", + "mpl.figure.prototype.send_message = function (type, properties) {\n", + " properties['type'] = type;\n", + " properties['figure_id'] = this.id;\n", + " this.ws.send(JSON.stringify(properties));\n", + "};\n", + "\n", + "mpl.figure.prototype.send_draw_message = function () {\n", + " if (!this.waiting) {\n", + " this.waiting = true;\n", + " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", + " var format_dropdown = fig.format_dropdown;\n", + " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", + " fig.ondownload(fig, format);\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", + " var size = msg['size'];\n", + " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", + " fig._resize_canvas(size[0], size[1], msg['forward']);\n", + " fig.send_message('refresh', {});\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", + " var x0 = msg['x0'] / fig.ratio;\n", + " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", + " var x1 = msg['x1'] / fig.ratio;\n", + " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", + " x0 = Math.floor(x0) + 0.5;\n", + " y0 = Math.floor(y0) + 0.5;\n", + " x1 = Math.floor(x1) + 0.5;\n", + " y1 = Math.floor(y1) + 0.5;\n", + " var min_x = Math.min(x0, x1);\n", + " var min_y = Math.min(y0, y1);\n", + " var width = Math.abs(x1 - x0);\n", + " var height = Math.abs(y1 - y0);\n", + "\n", + " fig.rubberband_context.clearRect(\n", + " 0,\n", + " 0,\n", + " fig.canvas.width / fig.ratio,\n", + " fig.canvas.height / fig.ratio\n", + " );\n", + "\n", + " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", + " // Updates the figure title.\n", + " fig.header.textContent = msg['label'];\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", + " var cursor = msg['cursor'];\n", + " switch (cursor) {\n", + " case 0:\n", + " cursor = 'pointer';\n", + " break;\n", + " case 1:\n", + " cursor = 'default';\n", + " break;\n", + " case 2:\n", + " cursor = 'crosshair';\n", + " break;\n", + " case 3:\n", + " cursor = 'move';\n", + " break;\n", + " }\n", + " fig.rubberband_canvas.style.cursor = cursor;\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_message = function (fig, msg) {\n", + " fig.message.textContent = msg['message'];\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", + " // Request the server to send over a new figure.\n", + " fig.send_draw_message();\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", + " fig.image_mode = msg['mode'];\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", + " for (var key in msg) {\n", + " if (!(key in fig.buttons)) {\n", + " continue;\n", + " }\n", + " fig.buttons[key].disabled = !msg[key];\n", + " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", + " if (msg['mode'] === 'PAN') {\n", + " fig.buttons['Pan'].classList.add('active');\n", + " fig.buttons['Zoom'].classList.remove('active');\n", + " } else if (msg['mode'] === 'ZOOM') {\n", + " fig.buttons['Pan'].classList.remove('active');\n", + " fig.buttons['Zoom'].classList.add('active');\n", + " } else {\n", + " fig.buttons['Pan'].classList.remove('active');\n", + " fig.buttons['Zoom'].classList.remove('active');\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.updated_canvas_event = function () {\n", + " // Called whenever the canvas gets updated.\n", + " this.send_message('ack', {});\n", + "};\n", + "\n", + "// A function to construct a web socket function for onmessage handling.\n", + "// Called in the figure constructor.\n", + "mpl.figure.prototype._make_on_message_function = function (fig) {\n", + " return function socket_on_message(evt) {\n", + " if (evt.data instanceof Blob) {\n", + " /* FIXME: We get \"Resource interpreted as Image but\n", + " * transferred with MIME type text/plain:\" errors on\n", + " * Chrome. But how to set the MIME type? It doesn't seem\n", + " * to be part of the websocket stream */\n", + " evt.data.type = 'image/png';\n", + "\n", + " /* Free the memory for the previous frames */\n", + " if (fig.imageObj.src) {\n", + " (window.URL || window.webkitURL).revokeObjectURL(\n", + " fig.imageObj.src\n", + " );\n", + " }\n", + "\n", + " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", + " evt.data\n", + " );\n", + " fig.updated_canvas_event();\n", + " fig.waiting = false;\n", + " return;\n", + " } else if (\n", + " typeof evt.data === 'string' &&\n", + " evt.data.slice(0, 21) === 'data:image/png;base64'\n", + " ) {\n", + " fig.imageObj.src = evt.data;\n", + " fig.updated_canvas_event();\n", + " fig.waiting = false;\n", + " return;\n", + " }\n", + "\n", + " var msg = JSON.parse(evt.data);\n", + " var msg_type = msg['type'];\n", + "\n", + " // Call the \"handle_{type}\" callback, which takes\n", + " // the figure and JSON message as its only arguments.\n", + " try {\n", + " var callback = fig['handle_' + msg_type];\n", + " } catch (e) {\n", + " console.log(\n", + " \"No handler for the '\" + msg_type + \"' message type: \",\n", + " msg\n", + " );\n", + " return;\n", + " }\n", + "\n", + " if (callback) {\n", + " try {\n", + " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", + " callback(fig, msg);\n", + " } catch (e) {\n", + " console.log(\n", + " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", + " e,\n", + " e.stack,\n", + " msg\n", + " );\n", + " }\n", + " }\n", + " };\n", + "};\n", + "\n", + "// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n", + "mpl.findpos = function (e) {\n", + " //this section is from http://www.quirksmode.org/js/events_properties.html\n", + " var targ;\n", + " if (!e) {\n", + " e = window.event;\n", + " }\n", + " if (e.target) {\n", + " targ = e.target;\n", + " } else if (e.srcElement) {\n", + " targ = e.srcElement;\n", + " }\n", + " if (targ.nodeType === 3) {\n", + " // defeat Safari bug\n", + " targ = targ.parentNode;\n", + " }\n", + "\n", + " // pageX,Y are the mouse positions relative to the document\n", + " var boundingRect = targ.getBoundingClientRect();\n", + " var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n", + " var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n", + "\n", + " return { x: x, y: y };\n", + "};\n", + "\n", + "/*\n", + " * return a copy of an object with only non-object keys\n", + " * we need this to avoid circular references\n", + " * http://stackoverflow.com/a/24161582/3208463\n", + " */\n", + "function simpleKeys(original) {\n", + " return Object.keys(original).reduce(function (obj, key) {\n", + " if (typeof original[key] !== 'object') {\n", + " obj[key] = original[key];\n", + " }\n", + " return obj;\n", + " }, {});\n", + "}\n", + "\n", + "mpl.figure.prototype.mouse_event = function (event, name) {\n", + " var canvas_pos = mpl.findpos(event);\n", + "\n", + " if (name === 'button_press') {\n", + " this.canvas.focus();\n", + " this.canvas_div.focus();\n", + " }\n", + "\n", + " var x = canvas_pos.x * this.ratio;\n", + " var y = canvas_pos.y * this.ratio;\n", + "\n", + " this.send_message(name, {\n", + " x: x,\n", + " y: y,\n", + " button: event.button,\n", + " step: event.step,\n", + " guiEvent: simpleKeys(event),\n", + " });\n", + "\n", + " /* This prevents the web browser from automatically changing to\n", + " * the text insertion cursor when the button is pressed. We want\n", + " * to control all of the cursor setting manually through the\n", + " * 'cursor' event from matplotlib */\n", + " event.preventDefault();\n", + " return false;\n", + "};\n", + "\n", + "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", + " // Handle any extra behaviour associated with a key event\n", + "};\n", + "\n", + "mpl.figure.prototype.key_event = function (event, name) {\n", + " // Prevent repeat events\n", + " if (name === 'key_press') {\n", + " if (event.which === this._key) {\n", + " return;\n", + " } else {\n", + " this._key = event.which;\n", + " }\n", + " }\n", + " if (name === 'key_release') {\n", + " this._key = null;\n", + " }\n", + "\n", + " var value = '';\n", + " if (event.ctrlKey && event.which !== 17) {\n", + " value += 'ctrl+';\n", + " }\n", + " if (event.altKey && event.which !== 18) {\n", + " value += 'alt+';\n", + " }\n", + " if (event.shiftKey && event.which !== 16) {\n", + " value += 'shift+';\n", + " }\n", + "\n", + " value += 'k';\n", + " value += event.which.toString();\n", + "\n", + " this._key_event_extra(event, name);\n", + "\n", + " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", + " return false;\n", + "};\n", + "\n", + "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", + " if (name === 'download') {\n", + " this.handle_save(this, null);\n", + " } else {\n", + " this.send_message('toolbar_button', { name: name });\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", + " this.message.textContent = tooltip;\n", + "};\n", + "\n", + "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", + "// prettier-ignore\n", + "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", + "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n", + "\n", + "mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n", + "\n", + "mpl.default_extension = \"png\";/* global mpl */\n", + "\n", + "var comm_websocket_adapter = function (comm) {\n", + " // Create a \"websocket\"-like object which calls the given IPython comm\n", + " // object with the appropriate methods. Currently this is a non binary\n", + " // socket, so there is still some room for performance tuning.\n", + " var ws = {};\n", + "\n", + " ws.close = function () {\n", + " comm.close();\n", + " };\n", + " ws.send = function (m) {\n", + " //console.log('sending', m);\n", + " comm.send(m);\n", + " };\n", + " // Register the callback with on_msg.\n", + " comm.on_msg(function (msg) {\n", + " //console.log('receiving', msg['content']['data'], msg);\n", + " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", + " ws.onmessage(msg['content']['data']);\n", + " });\n", + " return ws;\n", + "};\n", + "\n", + "mpl.mpl_figure_comm = function (comm, msg) {\n", + " // This is the function which gets called when the mpl process\n", + " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", + "\n", + " var id = msg.content.data.id;\n", + " // Get hold of the div created by the display call when the Comm\n", + " // socket was opened in Python.\n", + " var element = document.getElementById(id);\n", + " var ws_proxy = comm_websocket_adapter(comm);\n", + "\n", + " function ondownload(figure, _format) {\n", + " window.open(figure.canvas.toDataURL());\n", + " }\n", + "\n", + " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", + "\n", + " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", + " // web socket which is closed, not our websocket->open comm proxy.\n", + " ws_proxy.onopen();\n", + "\n", + " fig.parent_element = element;\n", + " fig.cell_info = mpl.find_output_cell(\"
\");\n", + " if (!fig.cell_info) {\n", + " console.error('Failed to find cell for figure', id, fig);\n", + " return;\n", + " }\n", + " fig.cell_info[0].output_area.element.on(\n", + " 'cleared',\n", + " { fig: fig },\n", + " fig._remove_fig_handler\n", + " );\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_close = function (fig, msg) {\n", + " var width = fig.canvas.width / fig.ratio;\n", + " fig.cell_info[0].output_area.element.off(\n", + " 'cleared',\n", + " fig._remove_fig_handler\n", + " );\n", + " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", + "\n", + " // Update the output cell to use the data from the current canvas.\n", + " fig.push_to_output();\n", + " var dataURL = fig.canvas.toDataURL();\n", + " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", + " // the notebook keyboard shortcuts fail.\n", + " IPython.keyboard_manager.enable();\n", + " fig.parent_element.innerHTML =\n", + " '';\n", + " fig.close_ws(fig, msg);\n", + "};\n", + "\n", + "mpl.figure.prototype.close_ws = function (fig, msg) {\n", + " fig.send_message('closing', msg);\n", + " // fig.ws.close()\n", + "};\n", + "\n", + "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", + " // Turn the data on the canvas into data in the output cell.\n", + " var width = this.canvas.width / this.ratio;\n", + " var dataURL = this.canvas.toDataURL();\n", + " this.cell_info[1]['text/html'] =\n", + " '';\n", + "};\n", + "\n", + "mpl.figure.prototype.updated_canvas_event = function () {\n", + " // Tell IPython that the notebook contents must change.\n", + " IPython.notebook.set_dirty(true);\n", + " this.send_message('ack', {});\n", + " var fig = this;\n", + " // Wait a second, then push the new image to the DOM so\n", + " // that it is saved nicely (might be nice to debounce this).\n", + " setTimeout(function () {\n", + " fig.push_to_output();\n", + " }, 1000);\n", + "};\n", + "\n", + "mpl.figure.prototype._init_toolbar = function () {\n", + " var fig = this;\n", + "\n", + " var toolbar = document.createElement('div');\n", + " toolbar.classList = 'btn-toolbar';\n", + " this.root.appendChild(toolbar);\n", + "\n", + " function on_click_closure(name) {\n", + " return function (_event) {\n", + " return fig.toolbar_button_onclick(name);\n", + " };\n", + " }\n", + "\n", + " function on_mouseover_closure(tooltip) {\n", + " return function (event) {\n", + " if (!event.currentTarget.disabled) {\n", + " return fig.toolbar_button_onmouseover(tooltip);\n", + " }\n", + " };\n", + " }\n", + "\n", + " fig.buttons = {};\n", + " var buttonGroup = document.createElement('div');\n", + " buttonGroup.classList = 'btn-group';\n", + " var button;\n", + " for (var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " /* Instead of a spacer, we start a new button group. */\n", + " if (buttonGroup.hasChildNodes()) {\n", + " toolbar.appendChild(buttonGroup);\n", + " }\n", + " buttonGroup = document.createElement('div');\n", + " buttonGroup.classList = 'btn-group';\n", + " continue;\n", + " }\n", + "\n", + " button = fig.buttons[name] = document.createElement('button');\n", + " button.classList = 'btn btn-default';\n", + " button.href = '#';\n", + " button.title = name;\n", + " button.innerHTML = '';\n", + " button.addEventListener('click', on_click_closure(method_name));\n", + " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", + " buttonGroup.appendChild(button);\n", + " }\n", + "\n", + " if (buttonGroup.hasChildNodes()) {\n", + " toolbar.appendChild(buttonGroup);\n", + " }\n", + "\n", + " // Add the status bar.\n", + " var status_bar = document.createElement('span');\n", + " status_bar.classList = 'mpl-message pull-right';\n", + " toolbar.appendChild(status_bar);\n", + " this.message = status_bar;\n", + "\n", + " // Add the close button to the window.\n", + " var buttongrp = document.createElement('div');\n", + " buttongrp.classList = 'btn-group inline pull-right';\n", + " button = document.createElement('button');\n", + " button.classList = 'btn btn-mini btn-primary';\n", + " button.href = '#';\n", + " button.title = 'Stop Interaction';\n", + " button.innerHTML = '';\n", + " button.addEventListener('click', function (_evt) {\n", + " fig.handle_close(fig, {});\n", + " });\n", + " button.addEventListener(\n", + " 'mouseover',\n", + " on_mouseover_closure('Stop Interaction')\n", + " );\n", + " buttongrp.appendChild(button);\n", + " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", + " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", + "};\n", + "\n", + "mpl.figure.prototype._remove_fig_handler = function (event) {\n", + " var fig = event.data.fig;\n", + " if (event.target !== this) {\n", + " // Ignore bubbled events from children.\n", + " return;\n", + " }\n", + " fig.close_ws(fig, {});\n", + "};\n", + "\n", + "mpl.figure.prototype._root_extra_style = function (el) {\n", + " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", + "};\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function (el) {\n", + " // this is important to make the div 'focusable\n", + " el.setAttribute('tabindex', 0);\n", + " // reach out to IPython and tell the keyboard manager to turn it's self\n", + " // off when our div gets focus\n", + "\n", + " // location in version 3\n", + " if (IPython.notebook.keyboard_manager) {\n", + " IPython.notebook.keyboard_manager.register_events(el);\n", + " } else {\n", + " // location in version 2\n", + " IPython.keyboard_manager.register_events(el);\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", + " var manager = IPython.notebook.keyboard_manager;\n", + " if (!manager) {\n", + " manager = IPython.keyboard_manager;\n", + " }\n", + "\n", + " // Check for shift+enter\n", + " if (event.shiftKey && event.which === 13) {\n", + " this.canvas_div.blur();\n", + " // select the cell after this one\n", + " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", + " IPython.notebook.select(index + 1);\n", + " }\n", + "};\n", + "\n", + "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", + " fig.ondownload(fig, null);\n", + "};\n", + "\n", + "mpl.find_output_cell = function (html_output) {\n", + " // Return the cell and output element which can be found *uniquely* in the notebook.\n", + " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", + " // IPython event is triggered only after the cells have been serialised, which for\n", + " // our purposes (turning an active figure into a static one), is too late.\n", + " var cells = IPython.notebook.get_cells();\n", + " var ncells = cells.length;\n", + " for (var i = 0; i < ncells; i++) {\n", + " var cell = cells[i];\n", + " if (cell.cell_type === 'code') {\n", + " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", + " var data = cell.output_area.outputs[j];\n", + " if (data.data) {\n", + " // IPython >= 3 moved mimebundle to data attribute of output\n", + " data = data.data;\n", + " }\n", + " if (data['text/html'] === html_output) {\n", + " return [cell, data, j];\n", + " }\n", + " }\n", + " }\n", + " }\n", + "};\n", + "\n", + "// Register the function which deals with the matplotlib target/channel.\n", + "// The kernel may be null if the page has been refreshed.\n", + "if (IPython.notebook.kernel !== null) {\n", + " IPython.notebook.kernel.comm_manager.register_target(\n", + " 'matplotlib',\n", + " mpl.mpl_figure_comm\n", + " );\n", + "}\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 32, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\n", + "def read_nexus(file_name):\n", + " file = h5py.File(file_name,'r')\n", + " groups = find_NXgroup(file)\n", + "\n", + " if find_nexus_class(groups, 'NXentry') is None:\n", + " print('This is not a NeXus file system')\n", + " \n", + " data_group = find_nexus_class(groups, 'NXdata')\n", + " data_dict = dict(data_group.attrs)\n", + " if 'signal' in data_dict:\n", + " signal = data_dict['signal']\n", + " if isinstance(signal, np.bytes_):\n", + " signal = signal.decode('UTF-8')\n", + " print(data_group[data_dict['signal']])\n", + " data = data_group[data_dict['signal']][()]\n", + " if 'axes' in data_dict:\n", + " for axis in data_dict['axes']:\n", + " if isinstance(axis, np.bytes_):\n", + " axis = axis.decode('UTF-8')\n", + " print(data_group[axis][()])\n", + " print(dict(data_group[axis].attrs))\n", + "\n", + " dataset = sidpy.Dataset.from_array(data)\n", + " \n", + " for i, \n", + " dataset.set_dimension(0, sidpy.Dimension(np.arange(dataset.shape[0]), 'x',\n", + " units='nm', quantity='Length',\n", + " dimension_type='spatial'))\n", + "dataset.set_dimension(1, sidpy.Dimension(np.linspace(-2, 2, num=dataset.shape[1], endpoint=True), 'y', \n", + " units='nm', quantity='Length',\n", + " dimension_type='spatial'))\n", + "dataset.set_dimension(2, sidpy.Dimension(np.sin(np.linspace(0, 2 * np.pi, num=dataset.shape[2])), 'bias',\n", + " units='mV', quantity='Voltage',\n", + " dimension_type='spectral'))\n", + " \n", + " \n", + " return dataset\n", + "\n", + "\n", + "\n", + "dataset = read_nexus('example_data/33id_spec_22_2D.hdf5')\n", + " \n", + "print(data_group.name)\n", + "print(data_dict['chi_indices'])\n", + "print(data_dict)\n", + "plt.figure()\n", + "plt.imshow(dataset)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a1f8df6e", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 134, + "id": "399c5064", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Epoch \n", + "H \n", + "I0 \n", + "I00 \n", + "I0_1 \n", + "K \n", + "Kalpha \n", + "L \n", + "_mca_ \n", + "_mca_channel_ \n", + "chi \n", + "elastic \n", + "eta \n", + "harmonic \n", + "seconds \n", + "signal \n", + "signal2 \n" + ] + } + ], + "source": [ + "for key in data_group:\n", + " print(key, ( data_group[key]))" + ] + }, + { + "cell_type": "code", + "execution_count": 78, + "id": "ad95c091", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " dict_keys(['HDF5_Version', 'SPEC_comments', 'SPEC_date', 'SPEC_epoch', 'SPEC_file', 'SPEC_num_headers', 'SPEC_user', 'default', 'h5py_version', 'numpy_version', 'spec2nexus_version'])\n", + "--- found entry\n" + ] + } + ], + "source": [ + "print(file, dict(file.attrs).keys())\n", + "\n", + "for group in groups:\n", + " if dict(group.attrs)['NX_class'] == 'NXentry':\n", + " print ('--- found entry')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b930120a", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.8" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pyNSID/__init__.py b/pyNSID/__init__.py index 5ae4e6a..700143c 100644 --- a/pyNSID/__init__.py +++ b/pyNSID/__init__.py @@ -1,10 +1,6 @@ -from . import io, processing, viz +from . import io from .io import * -from .processing import * -from .viz import * from .__version__ import version as __version__ -__all__ = ['__version__', 'io', 'processing', 'viz'] +__all__ = ['__version__', 'io'] __all__ += io.__all__ -__all__ += processing.__all__ -__all__ += viz.__all__ diff --git a/pyNSID/__version__.py b/pyNSID/__version__.py index 5edeabf..b78fe2a 100644 --- a/pyNSID/__version__.py +++ b/pyNSID/__version__.py @@ -1,2 +1,2 @@ -version = '0.0.2' -time = '2021-01-08 16:55:25' +version = '0.0.3' +time = '2021-10-15 16:55:25' diff --git a/pyNSID/io/__init__.py b/pyNSID/io/__init__.py index 8bf5925..3392a41 100644 --- a/pyNSID/io/__init__.py +++ b/pyNSID/io/__init__.py @@ -14,5 +14,6 @@ from . import hdf_utils, hdf_io from .nsi_reader import NSIDReader from .hdf_io import * +from .hdf_utils import make_nexus_compatible -__all__ = ['hdf_utils', 'hdf_io', 'NSIDReader'] \ No newline at end of file +__all__ = ['hdf_utils', 'hdf_io', 'NSIDReader', 'make_nexus_compatible'] \ No newline at end of file diff --git a/pyNSID/io/hdf_io.py b/pyNSID/io/hdf_io.py index 7fd68d8..46d3680 100644 --- a/pyNSID/io/hdf_io.py +++ b/pyNSID/io/hdf_io.py @@ -180,7 +180,7 @@ def write_nsid_dataset(dataset, h5_group, main_data_name='', verbose=False, for attr_name in dir(dataset): attr_val = getattr(dataset, attr_name) - if isinstance(attr_val, dict): + if isinstance(attr_val, dict) and attr_name[0] != '_': if verbose: print('Writing attributes from property: {} of the ' 'sidpy.Dataset'.format(attr_name)) @@ -258,6 +258,6 @@ def write_results(h5_group, dataset=None, attributes=None, process_name=None): write_nsid_dataset(dset, log_group) if found_valid_attributes: - write_simple_attrs(log_group, flatten_dict(attributes)) + write_simple_attrs(log_group, attributes) return log_group diff --git a/pyNSID/io/hdf_utils.py b/pyNSID/io/hdf_utils.py index 44fc3db..e26d7c1 100644 --- a/pyNSID/io/hdf_utils.py +++ b/pyNSID/io/hdf_utils.py @@ -12,11 +12,10 @@ from warnings import warn import h5py import numpy as np +import datetime -from sidpy.base.dict_utils import nest_dict -# from sidpy.base.string_utils import validate_single_string_arg from sidpy.hdf.hdf_utils import get_attr, copy_dataset, write_simple_attrs, \ - write_book_keeping_attrs + write_book_keeping_attrs, h5_group_to_dict from sidpy.hdf import hdf_utils as hut from sidpy import Dimension, Dataset @@ -124,8 +123,8 @@ def read_h5py_dataset(dset): for key in dset.parent: if isinstance(dset.parent[key], h5py.Group): if key[0] != '_': - setattr(dataset, key, nest_dict(dset.parent[key].attrs)) - + setattr(dataset, key, h5_group_to_dict(dset.parent[key])) + dataset.h5_dataset = dset dataset.h5_filename = dset.file.filename try: @@ -476,3 +475,57 @@ def write_pynsid_book_keeping_attrs(h5_object): """ write_book_keeping_attrs(h5_object) write_simple_attrs(h5_object, {'pyNSID_version': pynsid_version}) + + +def make_nexus_compatible(h5_dataset): + """ + Makes a pyNSID file compatible with the NeXus file format + by adding the approbriate attributes and by writing one group. + + Parameters + ---------- + h5_dataset: h5py.Dataset + h5py dataset with main data + + Returns + ------- + + """ + if not isinstance(h5_dataset, h5py.Dataset): + raise ValueError('We need a h5py dataset for compatibility with NeXus file format') + + time_stamp = "T".join(str(datetime.datetime.now()).split()) + h5_file = h5_dataset.file + h5_group = h5_dataset.parent.parent + h5_file.attrs[u'default'] = h5_dataset.parent.parent.name + + # give the HDF5 root some more attributes + + h5_file.attrs[u'file_name'] = h5_file.filename + h5_file.attrs[u'file_time'] = time_stamp + h5_file.attrs[u'instrument'] = u'None' + h5_file.attrs[u'creator'] = u'pyNSID' + h5_file.attrs[u'NeXus_version'] = u'4.3.0' + h5_file.attrs[u'HDF5_Version'] = h5py.version.hdf5_version + h5_file.attrs[u'h5py_version'] = h5py.version.version + + h5_file.attrs[u'default'] = h5_group.name + + h5_group.attrs[u'NX_class'] = u'NXentry' + h5_group.attrs[u'default'] = h5_dataset.name.split('/')[-1] + + if 'title' in h5_group: + del h5_group['title'] + h5_group.create_dataset(u'title', data=h5_dataset.name.split('/')[-1]) + + nxdata = h5_dataset.parent + + nxdata.attrs[u'NX_class'] = u'NXdata' + nxdata.attrs[u'signal'] = h5_dataset.name.split('/')[-1] + axes = [] + for dimension_label in h5_dataset.attrs['DIMENSION_LABELS']: + axes.append(dimension_label.decode('utf8')) + + nxdata.attrs[u'axes'] = axes + for i, axis in enumerate(axes): + nxdata.attrs[axes[i] + '_indices'] = [i, ] diff --git a/pyNSID/io/nsi_reader.py b/pyNSID/io/nsi_reader.py index f825eed..4198d85 100644 --- a/pyNSID/io/nsi_reader.py +++ b/pyNSID/io/nsi_reader.py @@ -38,7 +38,7 @@ def __init__(self, file_path): the file again outside the context of this Reader. """ - warn('This Reader will eventually be moved to the ScopeReaders package' + warn('This Reader will be moved to the ScifiReaders package in next release.' '. Be prepared to change your import statements', FutureWarning) diff --git a/pyNSID/processing/__init__.py b/pyNSID/processing/__init__.py deleted file mode 100644 index 912b011..0000000 --- a/pyNSID/processing/__init__.py +++ /dev/null @@ -1,14 +0,0 @@ -""" -Formalizing data processing on NSID datasets using parallel computing tools - -Submodules ----------- - -.. autosummary:: - :toctree: _autosummary - -""" - -#from .process import Process - -__all__ = [] diff --git a/pyNSID/processing/process.py b/pyNSID/processing/process.py deleted file mode 100644 index e69de29..0000000 diff --git a/pyNSID/viz/__init__.py b/pyNSID/viz/__init__.py deleted file mode 100644 index d8cc14f..0000000 --- a/pyNSID/viz/__init__.py +++ /dev/null @@ -1,15 +0,0 @@ -""" -Tools for static and interactive visualization of USID main datasets and scientific imaging and spectroscopy data - -Submodules ----------- - -.. autosummary:: - :toctree: _autosummary - - - -""" - - -__all__ = [] diff --git a/tests/io/test_hdf_io.py b/tests/io/test_hdf_io.py index 5a7d21c..187edd7 100644 --- a/tests/io/test_hdf_io.py +++ b/tests/io/test_hdf_io.py @@ -5,7 +5,7 @@ import numpy as np from os import remove -sys.path.insert(0, "../../../sidpy/") +# sys.path.insert(0, "../../../sidpy/") import sidpy sys.path.insert(0, "../../") @@ -14,8 +14,7 @@ print(sidpy.__version__) - -#Suhas +# Suhas class TestCreateEmptyDataset(unittest.TestCase): def base_test(self, dims=3): @@ -68,7 +67,8 @@ def test_obj_with_same_name_already_exists_in_file(self): def test_name_kwarg_used_correctly(self): pass -#Gerd + +# Gerd class TestWriteNSIDataset(unittest.TestCase): def base_test(self, dims=3, dim_types=['spatial', 'spatial', 'spectral'], data_type='complex', verbose=True): @@ -87,11 +87,11 @@ def base_test(self, dims=3, dim_types=['spatial', 'spatial', 'spectral'], data = np.random.normal(size=shape) data = np.squeeze(np.array(data, dtype=np.float64)) - data_set = sidpy.Dataset.from_array(data[:], name='Image') + data_set = sidpy.Dataset.from_array(data[:], title='Image') for ind in range(dims): data_set.set_dimension(ind, sidpy.Dimension(np.linspace(-2, 2, num=data_set.shape[ind], endpoint=True), - name='x'+str(ind), units='um', quantity='Length', + title='x'+str(ind), units='um', quantity='Length', dimension_type=dim_types[ind])) data_set.units = 'nm' data_set.source = 'CypherEast2' @@ -138,7 +138,7 @@ def test_not_sidpy_dataset(self): pyNSID.hdf_io.write_nsid_dataset(h5_group) def test_not_h5_group(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') with self.assertRaises(TypeError): pyNSID.hdf_io.write_nsid_dataset(data_set) @@ -154,7 +154,7 @@ def test_not_h5_group(self): pyNSID.hdf_io.write_nsid_dataset(data_set, np.zeros([5, 6])) def test_main_data_name_not_str(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') @@ -162,7 +162,7 @@ def test_main_data_name_not_str(self): pyNSID.hdf_io.write_nsid_dataset(data_set, h5_group, main_data_name=2) def test_main_data_name_given(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') @@ -170,14 +170,14 @@ def test_main_data_name_given(self): self.assertTrue('good_name' in h5_group) def test_h5_file_in_read_only_mode(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'r') with self.assertRaises(ValueError): pyNSID.hdf_io.write_nsid_dataset(data_set, h5_file) def test_h5_file_closed(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') h5_file.close() @@ -186,7 +186,7 @@ def test_h5_file_closed(self): pyNSID.hdf_io.write_nsid_dataset(data_set, h5_group) def test_group_already_has_obj_same_name_as_main_dset(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') occupied = h5_group.create_group('occupied') @@ -194,13 +194,13 @@ def test_group_already_has_obj_same_name_as_main_dset(self): pyNSID.hdf_io.write_nsid_dataset(data_set, h5_group, main_data_name='occupied') def test_group_already_has_dim_h5_dset_diff_lengths(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') pyNSID.hdf_io.write_nsid_dataset(data_set, h5_group) - data_set = sidpy.Dataset.from_array(np.zeros([7, 8]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([7, 8]), title='Image') with self.assertRaises(ValueError): pyNSID.hdf_io.write_nsid_dataset(data_set, h5_group) @@ -211,16 +211,17 @@ def test_group_already_has_dim_h5_dset_correct(self): pass def test_complex_valued_main_dset(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6], dtype=complex), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6], dtype=complex), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') pyNSID.hdf_io.write_nsid_dataset(data_set, h5_group) - print(h5_group['Image']['Image'][()].dtype) + print(h5_group) # ['Image'][()].dtype) + sidpy.hdf_utils.print_tree(h5_file) self.assertTrue(h5_group['Image']['Image'][()].dtype == np.complex) def test_complex_valued_dimension(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6], dtype=complex), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6], dtype=complex), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') data_set.set_dimension(0, sidpy.Dimension(np.arange(5, dtype=complex))) @@ -233,7 +234,7 @@ def test_book_keeping_attrs_written_to_group(self): data = np.random.normal(size=shape) h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:], name='Image') + data_set = sidpy.Dataset.from_array(data[:], title='Image') sidpy.hdf_utils.write_book_keeping_attrs(h5_group) hdf_io.write_nsid_dataset(data_set, h5_group, main_data_name='data_1') for attr in ['machine_id', 'platform', 'sidpy_version', 'timestamp']: @@ -254,7 +255,7 @@ def test_no_metadata(self): remove('test2.h5') def test_metadata_is_empty(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') data_set.metadata = {} @@ -264,7 +265,7 @@ def test_metadata_is_empty(self): self.assertFalse('metadata' in h5_group['Image']) def test_has_metadata_dict(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') data_set.metadata = {'some': 'thing'} @@ -276,7 +277,7 @@ def test_has_metadata_dict(self): # def test_metadata_not_dict(self): # is actually tested in sidpy def test_metadata_is_nested(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') data_set.metadata = {'some': {'some': 'thing'}} @@ -286,12 +287,13 @@ def test_metadata_is_nested(self): self.assertTrue('metadata' in h5_group['Image']) print(h5_group['Image']['metadata'].attrs.keys()) - self.assertTrue(dict(h5_group['Image']['metadata'].attrs) == {'some-some': 'thing'}) + read_dict = sidpy.hdf_utils.h5_group_to_dict(h5_group['Image']['metadata']) + self.assertTrue(read_dict['metadata']['some'] == {'some': 'thing'}) # def test_no_original_metadata(self): # cannot delete attribute delattr(data_set, 'original_metadata') def test_original_metadata_is_empty(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') data_set.original_metadata = {} @@ -301,7 +303,7 @@ def test_original_metadata_is_empty(self): self.assertFalse('original_metadata' in h5_group['Image']) def test_has_original_metadata_dict(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') data_set.original_metadata = {'some': 'thing'} @@ -313,7 +315,7 @@ def test_has_original_metadata_dict(self): # def test_original_metadata_not_dict(self): # tested in sidpy def test_original_metadata_is_nested(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') data_set.original_metadata = {'some': {'some': 'thing'}} @@ -321,12 +323,14 @@ def test_original_metadata_is_nested(self): pyNSID.hdf_io.write_nsid_dataset(data_set, h5_group) self.assertTrue('original_metadata' in h5_group['Image']) - self.assertTrue(dict(h5_group['Image']['original_metadata'].attrs) == {'some-some': 'thing'}) + + read_dict = sidpy.hdf_utils.h5_group_to_dict(h5_group['Image']['original_metadata']) + self.assertTrue(read_dict['original_metadata']['some'] == {'some': 'thing'}) # TODO check if datasets are indeed linked correctly to main def test_h5_dataset_property_of_sidpy_dataset_populated(self): - data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), name='Image') + data_set = sidpy.Dataset.from_array(np.zeros([5, 6]), title='Image') h5_file = h5py.File('test.h5', 'w') h5_group = h5_file.create_group('MyGroup') data_set.property = {'some': {'some': 'thing'}} @@ -353,7 +357,7 @@ def test_not_h5py_group_obj(self): h5_group = [10,115] shape = (5, 15, 16) data = np.random.randn(shape[0], shape[1], shape[2]) - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') with self.assertRaises(TypeError): hdf_io.write_results(h5_group, dataset=data_set, attributes=None, process_name='TestProcess') @@ -363,18 +367,18 @@ def test_group_already_contains_objects_name_clashes(self): h5_group = h5_file.create_group('MyGroup') shape = (5, 15, 16) data = np.random.randn(shape[0], shape[1], shape[2]) - data_set1 = sidpy.Dataset.from_array(data[:, :, :], name='Image') - data_set2 = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set1 = sidpy.Dataset.from_array(data[:, :, :], title='Image') + data_set2 = sidpy.Dataset.from_array(data[:, :, :], title='Image') hdf_io.write_results(h5_group, dataset=data_set1, attributes=None, process_name='TestProcess') - #If we try to write data_set2 which has the same name, it probably should fail?? - #with self.assertRaises(ValueError): + # If we try to write data_set2 which has the same name, it probably should fail?? + # with self.assertRaises(ValueError): hdf_io.write_results(h5_group, dataset=data_set2, attributes=None, process_name='TestProcess') def test_no_sidpy_dataset_provided(self): h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - #going to pass a numpy array instead of a sidpy dataset + # going to pass a numpy array instead of a sidpy dataset with self.assertRaises(ValueError): hdf_io.write_results(h5_group, dataset=None, attributes=None, process_name='TestProcess') h5_file.close() @@ -396,7 +400,7 @@ def test_no_attributes_provided(self): data = np.random.normal(size=shape) h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') # pass data without attributes hdf_io.write_results(h5_group, dataset=data_set, attributes=None, process_name='TestProcess') @@ -409,7 +413,7 @@ def test_attributes_not_dict(self): data = np.random.normal(size=shape) h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') attributes = namedtuple('Dimensions', ['x', 'y']) # pass data with attributes being something other than dictionary @@ -423,7 +427,7 @@ def test_attributes_nested_dict(self): data = np.random.normal(size=shape) h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') attributes = {'Key1':10, 'Key2': np.linspace(0,1,10), 'NestedDict': {'KeyLevel2_0':10, 'KeyLevel2_1': np.linspace(0,1,10)}} @@ -455,7 +459,7 @@ def convert_flatten(d, parent_key='', sep='_'): data = np.random.normal(size=shape) h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') attributes = {'Key1': 10, 'Key2': np.linspace(0, 1, 10), 'NestedDict': {'KeyLevel2_0': 10, 'KeyLevel2_1': np.linspace(0, 1, 10)}} @@ -471,7 +475,7 @@ def test_process_name_not_str(self): data = np.random.normal(size=shape) h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') # pass data with process_name being something other than a string with self.assertRaises(TypeError): hdf_io.write_results(h5_group, dataset=data_set, attributes=None, process_name=['This shouldnt work']) @@ -483,7 +487,7 @@ def test_process_name_no_name_clashes(self): data = np.random.normal(size=shape) h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') # pass data with process_name being something other than a string hdf_io.write_results(h5_group, dataset=data_set, attributes=None, process_name='This should work') h5_file.close() @@ -499,7 +503,7 @@ def test_process_name_has_name_clashes(self): data = np.random.normal(size=shape) h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') # pass data with process_name being something other than a string hdf_io.write_results(h5_group, dataset=data_set, attributes=None, process_name='This should work') #Trying to rewrite with same process name should give us an error, not sure which type though! @@ -519,8 +523,8 @@ def test_multiple_sidpy_datasets_as_results(self): h5_file = h5py.File('test2.h5', 'w') h5_group = h5_file.create_group('MyGroup') - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') - data_set2 = sidpy.Dataset.from_array(data2[:, :, :], name='Image2') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') + data_set2 = sidpy.Dataset.from_array(data2[:, :, :], title='Image2') results = [data_set, data_set2] @@ -533,7 +537,7 @@ def test_simple(self): h5_group = h5_f.create_group('MyGroup') shape = (5, 15, 16) data = np.random.randn(shape[0], shape[1], shape[2]) - data_set = sidpy.Dataset.from_array(data[:, :, :], name='Image') + data_set = sidpy.Dataset.from_array(data[:, :, :], title='Image') hdf_io.write_results(h5_group, dataset=data_set, attributes=None, process_name='TestProcess') # TODO: Add some more assertions diff --git a/tests/processing/__init__.py b/tests/processing/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/tests/viz/__init__.py b/tests/viz/__init__.py deleted file mode 100644 index e69de29..0000000