Merge pull request #56 from jmtyszka/development

Development

CHANGELOG.md

@@ -1,6 +1,11 @@
 # BIDSKIT Changelog
 
-## Version 1.2
+## Version 1.2.3
+
+## Version 1.2.2
+- Fixed auto run number issue #55
+
+## Version 1.2.1
 
 - Bring output directory structure into compliance with BIDS v1.2
 - Old source/ directory contents raised to top level of BIDS dataset directory

README.md

@@ -1,4 +1,4 @@
-# BIDSKIT 1.2.2 
+# BIDSKIT 1.2.3 DEVELOPMENT 
 Python utilities for converting from DICOM to BIDS neuroimaging formats.
 
 The *bidskit* console command takes a directory tree containing imaging series from one or more subjects (eg T1w MPRAGE, BOLD EPI, Fieldmaps), converts the imaging data to Nifti-1 format with JSON metadata files (sidecars) and populates a
@@ -16,4 +16,4 @@ Let us know about bugs and feature requests through this repo's
 
 ## Related Projects
 - [heudiconv](https://github.com/nipy/heudiconv) General purpose heuristic DICOM converter
-- [dcm2bids](https://github.com/cbedetti/Dcm2Bids) Christophe Beddetti's DICOM to BIDS converter 
+- [dcm2bids](https://github.com/cbedetti/Dcm2Bids) Christophe Beddetti's DICOM to BIDS converter 

bidskit/bidstree.py

@@ -24,8 +24,6 @@
 SOFTWARE.
 """
 
-__version__ = '1.2.2'
-
 import os
 import sys
 import json

bidskit/io.py

@@ -24,8 +24,6 @@
 SOFTWARE.
 """
 
-__version__ = '1.2.2'
-
 import os
 import sys
 import shutil
@@ -46,8 +44,13 @@ def read_json(fname):
         json_dict = json.load(fd)
         fd.close()
     except IOError:
+        print('*** {}'.format(fname))
         print('*** JSON sidecar not found - returning empty dictionary')
         json_dict = dict()
+    except json.decoder.JSONDecodeError:
+        print('*** {}'.format(fname))
+        print('*** JSON sidecar decoding error - returning empty dictionary')
+        json_dict = dict()
 
     return json_dict
 

bidskit/launcher.py

@@ -42,7 +42,7 @@
 SOFTWARE.
 """
 
-__version__ = '1.2.2'
+__version__ = '1.2.3'
 
 import os
 import sys

bidskit/organize.py

@@ -24,8 +24,6 @@
 SOFTWARE.
 """
 
-__version__ = '1.2.2'
-
 import os
 import shutil
 import bidskit.translate as btr

bidskit/translate.py

@@ -24,8 +24,6 @@
 SOFTWARE.
 """
 
-__version__ = '1.2.2'
-
 import os
 import sys
 import json
@@ -72,7 +70,14 @@ def get_acq_time(json_file):
     """
 
     info = bio.read_json(json_file)
-    return info['AcquisitionTime']
+
+    if 'AcquisitionTime' in info:
+        acq_time = info['AcquisitionTime']
+    else:
+        print('* AcquisitionTime not found in {}'.format(json_file))
+        acq_time = "00:00:00.00"
+
+    return acq_time
 
 
 def prune_intendedfors(bids_subj_dir, fmap_only):

setup.py

@@ -45,7 +45,7 @@
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='1.2.2',  # Required
+    version='1.2.3',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field:

venv/bin/activate

@@ -0,0 +1,76 @@
+# This file must be used with "source bin/activate" *from bash*
+# you cannot run it directly
+
+deactivate () {
+    # reset old environment variables
+    if [ -n "${_OLD_VIRTUAL_PATH:-}" ] ; then
+        PATH="${_OLD_VIRTUAL_PATH:-}"
+        export PATH
+        unset _OLD_VIRTUAL_PATH
+    fi
+    if [ -n "${_OLD_VIRTUAL_PYTHONHOME:-}" ] ; then
+        PYTHONHOME="${_OLD_VIRTUAL_PYTHONHOME:-}"
+        export PYTHONHOME
+        unset _OLD_VIRTUAL_PYTHONHOME
+    fi
+
+    # This should detect bash and zsh, which have a hash command that must
+    # be called to get it to forget past commands.  Without forgetting
+    # past commands the $PATH changes we made may not be respected
+    if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
+        hash -r
+    fi
+
+    if [ -n "${_OLD_VIRTUAL_PS1:-}" ] ; then
+        PS1="${_OLD_VIRTUAL_PS1:-}"
+        export PS1
+        unset _OLD_VIRTUAL_PS1
+    fi
+
+    unset VIRTUAL_ENV
+    if [ ! "$1" = "nondestructive" ] ; then
+    # Self destruct!
+        unset -f deactivate
+    fi
+}
+
+# unset irrelevant variables
+deactivate nondestructive
+
+VIRTUAL_ENV="/Users/jmt/GitHub/bidskit/venv"
+export VIRTUAL_ENV
+
+_OLD_VIRTUAL_PATH="$PATH"
+PATH="$VIRTUAL_ENV/bin:$PATH"
+export PATH
+
+# unset PYTHONHOME if set
+# this will fail if PYTHONHOME is set to the empty string (which is bad anyway)
+# could use `if (set -u; : $PYTHONHOME) ;` in bash
+if [ -n "${PYTHONHOME:-}" ] ; then
+    _OLD_VIRTUAL_PYTHONHOME="${PYTHONHOME:-}"
+    unset PYTHONHOME
+fi
+
+if [ -z "${VIRTUAL_ENV_DISABLE_PROMPT:-}" ] ; then
+    _OLD_VIRTUAL_PS1="${PS1:-}"
+    if [ "x(venv) " != x ] ; then
+	PS1="(venv) ${PS1:-}"
+    else
+    if [ "`basename \"$VIRTUAL_ENV\"`" = "__" ] ; then
+        # special case for Aspen magic directories
+        # see http://www.zetadev.com/software/aspen/
+        PS1="[`basename \`dirname \"$VIRTUAL_ENV\"\``] $PS1"
+    else
+        PS1="(`basename \"$VIRTUAL_ENV\"`)$PS1"
+    fi
+    fi
+    export PS1
+fi
+
+# This should detect bash and zsh, which have a hash command that must
+# be called to get it to forget past commands.  Without forgetting
+# past commands the $PATH changes we made may not be respected
+if [ -n "${BASH:-}" -o -n "${ZSH_VERSION:-}" ] ; then
+    hash -r
+fi

venv/bin/activate.csh

@@ -0,0 +1,37 @@
+# This file must be used with "source bin/activate.csh" *from csh*.
+# You cannot run it directly.
+# Created by Davide Di Blasi <davidedb@gmail.com>.
+# Ported to Python 3.3 venv by Andrew Svetlov <andrew.svetlov@gmail.com>
+
+alias deactivate 'test $?_OLD_VIRTUAL_PATH != 0 && setenv PATH "$_OLD_VIRTUAL_PATH" && unset _OLD_VIRTUAL_PATH; rehash; test $?_OLD_VIRTUAL_PROMPT != 0 && set prompt="$_OLD_VIRTUAL_PROMPT" && unset _OLD_VIRTUAL_PROMPT; unsetenv VIRTUAL_ENV; test "\!:*" != "nondestructive" && unalias deactivate'
+
+# Unset irrelevant variables.
+deactivate nondestructive
+
+setenv VIRTUAL_ENV "/Users/jmt/GitHub/bidskit/venv"
+
+set _OLD_VIRTUAL_PATH="$PATH"
+setenv PATH "$VIRTUAL_ENV/bin:$PATH"
+
+
+set _OLD_VIRTUAL_PROMPT="$prompt"
+
+if (! "$?VIRTUAL_ENV_DISABLE_PROMPT") then
+    if ("venv" != "") then
+        set env_name = "venv"
+    else
+        if (`basename "VIRTUAL_ENV"` == "__") then
+            # special case for Aspen magic directories
+            # see http://www.zetadev.com/software/aspen/
+            set env_name = `basename \`dirname "$VIRTUAL_ENV"\``
+        else
+            set env_name = `basename "$VIRTUAL_ENV"`
+        endif
+    endif
+    set prompt = "[$env_name] $prompt"
+    unset env_name
+endif
+
+alias pydoc python -m pydoc
+
+rehash

venv/bin/activate.fish

@@ -0,0 +1,75 @@
+# This file must be used with ". bin/activate.fish" *from fish* (http://fishshell.org)
+# you cannot run it directly
+
+function deactivate  -d "Exit virtualenv and return to normal shell environment"
+    # reset old environment variables
+    if test -n "$_OLD_VIRTUAL_PATH"
+        set -gx PATH $_OLD_VIRTUAL_PATH
+        set -e _OLD_VIRTUAL_PATH
+    end
+    if test -n "$_OLD_VIRTUAL_PYTHONHOME"
+        set -gx PYTHONHOME $_OLD_VIRTUAL_PYTHONHOME
+        set -e _OLD_VIRTUAL_PYTHONHOME
+    end
+
+    if test -n "$_OLD_FISH_PROMPT_OVERRIDE"
+        functions -e fish_prompt
+        set -e _OLD_FISH_PROMPT_OVERRIDE
+        functions -c _old_fish_prompt fish_prompt
+        functions -e _old_fish_prompt
+    end
+
+    set -e VIRTUAL_ENV
+    if test "$argv[1]" != "nondestructive"
+        # Self destruct!
+        functions -e deactivate
+    end
+end
+
+# unset irrelevant variables
+deactivate nondestructive
+
+set -gx VIRTUAL_ENV "/Users/jmt/GitHub/bidskit/venv"
+
+set -gx _OLD_VIRTUAL_PATH $PATH
+set -gx PATH "$VIRTUAL_ENV/bin" $PATH
+
+# unset PYTHONHOME if set
+if set -q PYTHONHOME
+    set -gx _OLD_VIRTUAL_PYTHONHOME $PYTHONHOME
+    set -e PYTHONHOME
+end
+
+if test -z "$VIRTUAL_ENV_DISABLE_PROMPT"
+    # fish uses a function instead of an env var to generate the prompt.
+
+    # save the current fish_prompt function as the function _old_fish_prompt
+    functions -c fish_prompt _old_fish_prompt
+
+    # with the original prompt function renamed, we can override with our own.
+    function fish_prompt
+        # Save the return status of the last command
+        set -l old_status $status
+
+        # Prompt override?
+        if test -n "(venv) "
+            printf "%s%s" "(venv) " (set_color normal)
+        else
+            # ...Otherwise, prepend env
+            set -l _checkbase (basename "$VIRTUAL_ENV")
+            if test $_checkbase = "__"
+                # special case for Aspen magic directories
+                # see http://www.zetadev.com/software/aspen/
+                printf "%s[%s]%s " (set_color -b blue white) (basename (dirname "$VIRTUAL_ENV")) (set_color normal)
+            else
+                printf "%s(%s)%s" (set_color -b blue white) (basename "$VIRTUAL_ENV") (set_color normal)
+            end
+        end
+
+        # Restore the return status of the previous command.
+        echo "exit $old_status" | .
+        _old_fish_prompt
+    end
+
+    set -gx _OLD_FISH_PROMPT_OVERRIDE "$VIRTUAL_ENV"
+end

venv/pyvenv.cfg

@@ -0,0 +1,3 @@
+home = /usr/local/bin
+include-system-site-packages = true
+version = 3.7.3