[WIP] Adding Henke filters query tool

SpectroscoPyx/diagnostics/filters/filtersHenke.py

@@ -0,0 +1,216 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue May  1 20:13:55 2018
+
+Query tools for Henke filters site.
+
+@author: Pawel M. Kozlowski
+"""
+
+# python modules
+import numpy as np
+import requests as req
+import parse as parse
+import re
+import astropy.units as u
+import matplotlib.pyplot as plt
+
+
+
+#%% simple utilities
+
+# URL to nist ionization energy database
+henkeURL1 = 'http://henke.lbl.gov/optical_constants/filter2.html'
+henkeURL2 = 'http://henke.lbl.gov/cgi-bin/filter.pl'
+henkeURL3 = 'http://henke.lbl.gov/'
+
+# Checking website status
+#reqObj = req.post(henkeURL2)
+#print("STATUS:")
+#print(reqObj.status_code)
+#if reqObj.status_code == req.codes.ok:
+#    print("OK!")
+#else:
+#    print("CONNECTION FAILED!")
+#reqObj.raise_for_status()
+
+# for testing purposes only
+#print("HEADERS:")
+#print(reqObj.headers['content-type'])
+#print("ENCODING:")
+#print(reqObj.encoding)
+#print("TEXT:")
+#print(reqObj.text)
+
+
+#%% query tool(s)
+# list of default materials in Henke filters database
+# material name : (chemical formula, density in gm/cm^3)
+defaultMaterials = {'polyimide' : ('C22H10N2O5', 1.43),
+                    'boron nitride' : ('BN', 2.25),
+                    'silicon nitride' : ('Si3N4', 3.44),
+                    'polypropylene' : ('C3H6', 0.90),
+                    'PMMA' : ('C5H8O2', 1.19),
+                    'polycarbonate' : ('C16H14O3', 1.2),
+                    'mylar' : ('C10H8O4', 1.4),
+                    'Teflon' : ('C2F4', 2.2),
+                    'Parylene-C' : ('C8H7Cl', 1.29),
+                    'Parylene-N' : ('C8H8', 1.11)}
+
+
+
+def fetchLink(text):
+    """
+    Parses text resulting from Henke filter query to retrieve temporary
+    hyperlink to data table.
+    """
+    searchString = "<a HREF={}>"
+    tableStr = parse.search(searchString, text)
+    urlEnding = tableStr[0][2:-1]
+    fullURL = henkeURL3 + urlEnding
+    return fullURL
+
+
+def henkeParse(text):
+    """
+    Parses transmission data table from Henke filters page and returns
+    an array of values.
+    """
+    # split along new lines
+    splitText = text.splitlines()
+
+    # parsing first header line, which is of the form
+    # ' Cu Density=8.96 Thickness=0.2 microns'
+    header1 = splitText[0].strip().split(' ')
+    chemical = header1[0]
+    density = float(header1[1].split('=')[1])
+    thickness = float(header1[2].split('=')[1])
+
+
+    # parsing second header line, which is of the form
+    # ' Photon Energy (eV), Transmission'
+    header2 = splitText[1].strip().split(',')
+    spectralUnit = header2[0]
+
+
+    # getting array of transmission data strings
+    transmissionStr = splitText[2:]
+    # stripping whitespace on either side, splitting spectral and
+    # transmission values
+    transmissionStr2 = [transText.strip().split() for transText in transmissionStr]
+#    print(transmissionStr2)
+    # wrap into numpy array
+    transmissionArr = np.array(transmissionStr2)
+    # splitting spectral and transmission values into separate arrays
+    spectralStr = transmissionArr[:,0]
+    transmissionStr3 = transmissionArr[:,1]
+    # forcing transmission data to floats
+    spectralArr = [float(spect) for spect in spectralStr]
+    transmissionArr = [float(trans) for trans in transmissionStr3]
+    # adding units to transmission data
+    if spectralUnit == "Photon Energy (eV)":
+        spectralArr = spectralArr * u.eV
+    elif spectralUnit == "Wavelength (nm)":
+        spectralArr = spectralArr * u.nm
+    else:
+        raise Exception("Something changed with Henke site. Contact "
+                        "the developer to raise this bug as an issue.")
+    transmissionArr = transmissionArr * u.dimensionless_unscaled
+
+    return (spectralArr,
+            transmissionArr,
+            chemical,
+            density,
+            thickness,
+            spectralUnit)
+
+
+@u.quantity_input(density=u.g * u.cm ** -3,
+                  thickness=u.um)
+def queryHenke(formula="Si3N4",
+               density=-1 * u.g * u.cm ** -3,
+               thickness=0.2 * u.um,
+               spectralUnit="Energy",
+               minRange=10,
+               maxRange=1000,
+               npts=100,
+               plotScaling="Linear"):
+    """
+    Queries Henke filters page.
+    density defaults to -1, which uses tabulated values.
+    thickness defaults to 0.2 um.
+
+    """
+    # checking inputs
+    if not isinstance(formula, str):
+        raise ValueError("formula must be a string!")
+    # check if plot scaling is valid
+    if not plotScaling in ["Linear", "Log", "LogLin", "LinLog"]:
+        raise Exception(f"Invalid plot scaling {plotScaling} given.")
+    if minRange >= maxRange:
+        raise Exception("minRange must be less than maxRange!")
+    # ensuring spectral range is within limits of Henke tool
+    if spectralUnit == "Energy":
+        if minRange < 10 or maxRange > 30000:
+            raise Exception("Photon energies must be between 10 and 30,000 eV")
+    elif spectralUnit == "Wave":
+        if minRange < 0.041 or maxRange > 124:
+            raise Exception("Wavelengths must be between 0.041 and 124 nm")
+    else:
+        raise Exception(f"SpectralUnit must be either Energy or Wave, and "
+                        f"not {spectralUnit}")
+
+
+    # Starting requests session
+    with req.session() as s:
+        # values to be filled into website form
+        payload = {'Material': 'Enter Formula', # element and charge state
+                   'Formula': formula,
+                   'Density' : (density.to(u.g * u.cm ** -3)).value,
+                   'Thickness' : (thickness.to(u.um)).value,
+                   'Scan' : spectralUnit,
+                   'Min' : minRange,
+                   'Max' : maxRange,
+                   'Npts' : npts,
+                   'Plot' : plotScaling,
+                   'Output' : 'Plot'
+                   }
+        # website's repsonse to query
+        response1 = s.post(henkeURL2, data=payload)    
+        # extracting hyperlink to the transmission data table    
+        dataLink = fetchLink(response1.text)
+        # querying transmission data table
+        response2 = s.get(dataLink)
+    # parsing transmission data table
+    data = henkeParse(response2.text)
+    return data
+
+
+def henkeFilterPlot(data):
+    """
+    Takes data from queryHenke() and plots it.
+    """
+    plt.plot(data[0], data[1])
+    plt.xlabel(data[5])
+    plt.ylabel('Transmission')
+    plt.title(data[2])
+    plt.show()
+    return
+
+#%% testing query
+#data = queryHenke(formula="C",
+#                  thickness=1*u.um,
+#                  minRange=0.05,
+#                  maxRange=100,
+#                  npts=100,
+#                  spectralUnit="Wave")
+data = queryHenke(formula="C",
+                  thickness=1*u.um,
+                  minRange=10,
+                  maxRange=1000,
+                  npts=100,
+                  spectralUnit="Energy")
+
+henkeFilterPlot(data)
+