Uploaded working version

sl_io.py

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+import numpy as np
+
+from glob import glob
+from os import path
+
+
+def loadstack(hdrfile, master):
+    """Takes the full path to a STXM .hdr file as input.
+    Parses the .hdr file to get the energy points and the
+    dimensions of the image(s) and pixels.
+    
+    Builds a list of all existing raw image files associated
+    with the .hdr file and then loads each file.
+    
+    Returns the list of energies, the image dimensions, a stack
+    of raw images, and a list of existing image files.
+    """
+
+    with open(hdrfile, 'r') as hdr:
+        ln = hdr.readline()
+
+        while 'ScanDefinition' not in ln:
+            ln = hdr.readline()
+        scantype = ln.split(';')[1][9:-1]
+
+        while 'Axis = { Name = \"Energy\"' not in ln:
+            ln = hdr.readline()
+
+        ln = hdr.readline()
+        energies = ln[:ln.index(')')]
+        energies = energies.split(', ')
+        energies = [float(en) for en in energies[1:]]
+
+
+        if "Line Scan" in scantype:
+            while 'Axis = { Name = \"Sample\"' not in ln:
+                ln = hdr.readline()
+
+            ln = ln.split()
+            dims = [energies[-1] - energies[0], float(ln[ln.index('Max')+2][:-1]) - float(ln[ln.index('Min')+2][:-1]), 1.0, 1.0 ]
+            ln = hdr.readline()
+            ln = ln.split()
+            dims[2] = int(ln[ln.index('Points')+2][1:-1])
+            dims[3] = dims[1]/float(dims[2])
+
+        else:
+            while 'XRange = ' not in ln:
+                ln = hdr.readline()
+
+            ln = ln.split()
+            dims = [ln[ln.index(s) + 2] for s in ['XRange', 'YRange', 'XStep', 'YStep']]
+            dims = [float(d[:-1]) for d in dims]
+
+    workdir = path.dirname(hdrfile)
+    prefix = path.basename(hdrfile)[:-4]
+    ximlist = glob(path.join(workdir, prefix) + '*.xim')
+    ximlist.sort()
+    ximlist = [path.abspath(f) for f in ximlist]
+    raw = []
+    for k in range(len(ximlist)):
+        master.stackdisp.set('Loading image ' + str(k+1) + '/' + str(len(ximlist)))
+        master.master.update_idletasks()
+        raw.append(np.loadtxt(ximlist[k])[::-1])
+
+    return [energies, dims, raw, ximlist, scantype]
+
+def writencb(master):
+    """Writes stack files (.ncb and .dat) in aXis2000 format."""
+
+    fname = path.join(path.dirname(master.hdrfile), master.stackfname.get())
+    hdrfile = master.hdrfile
+    rawstack = master.data.rawstack
+    energies = master.data.energies
+
+    with open(hdrfile, 'r') as hdr:
+        ln = hdr.readline()
+
+        while ln[:12] != '{ CentreXPos':
+            ln = hdr.readline()
+        params = ln.split(';')
+
+        xdim = float(params[2][9:])
+        ydim = float(params[3][9:])
+        xnpx = int(params[6][10:])
+        ynpx = int(params[7][10:])
+
+        ringcurrent = []
+        imgids = []
+
+        hdr.readline()
+        while ln:
+            ln = hdr.readline()
+            if ln[:5] == 'Image':
+                params = ln.split('; ')
+                imgids.append(params[0][5:8])
+                ringcurrent.append(float(params[0][-6:]))
+
+    imgnames = [hdrfile[:-4] + '_a' + n + '.xim' for n in imgids]
+    print(len(imgnames), len(ringcurrent))
+    # normalize images to ring current 500.0
+    for i in range(len(rawstack)):
+        rawstack[i] *= 500.0
+        rawstack[i] /= ringcurrent[i]
+
+    alldata = np.array([])
+    for im in rawstack:
+        alldata = np.append(alldata, np.ndarray.flatten(im[::-1]))
+
+    # check max counts. if possible, scale up by power of 10,
+    # but keep the max counts below 32768 so that output can
+    # be stored as 16-bit integers. if max counts are above
+    # 32768, scale down by power of 10.
+
+    m = np.max(alldata)
+    scaleexp = np.log10(32767.0/m)
+    if scaleexp > 0:
+        scaleexp = int(scaleexp)
+    else:
+        scaleexp = int(scaleexp - 1)
+    scale = (10.0)**scaleexp
+
+    alldata *= scale
+
+    # write .ncb -- just a list of 16-bit integers
+    (alldata.astype('int16')).tofile(fname)
+
+    # write .dat file associated with .ncb. The pattern is:
+    #
+    #         [# of pixels in x]   [# of pixels in y]    [count scale factor]
+    #         0.00000              [x_width in microns]
+    #         0.00000              [y_width in microns]
+    #         [# of images]
+    #         [energy, image 1   ]
+    #         [energy, image 2   ]
+    #         [    ...           ]
+    #         [energy, last image]
+    #[filename, image 1]     [energy, image 1   ]   2.00  (<--- not sure what the function of this is!)
+    #[filename, image 2]     [energy, image 2   ]   2.00
+    #[    ...                                   ]   2.00
+    #[filename, last image]  [energy, last image]   2.00
+    #
+
+    datfile = open(fname[:-3] + 'dat', 'w')
+
+    datfile.write(' '*(12 - len(str(xnpx))) + str(xnpx))
+    datfile.write(' '*(12 - len(str(ynpx))) + str(ynpx))
+    datfile.write(' '*(13 - len(str(scale))) + str(scale))
+    datfile.write('\n')
+
+    datfile.write('     0.000000')
+    datfile.write(' '*(13 - len(str(xdim))) + str(xdim) + '\n')
+    datfile.write('     0.000000')
+    datfile.write(' '*(13 - len(str(ydim))) + str(ydim) + '\n')
+
+    datfile.write(' '*(12 - len(str(len(rawstack)))) + str(len(rawstack)) + '\n')
+
+    for i in range(len(rawstack)):
+        datfile.write(' '*(13 - len(str(energies[i]))) + str(energies[i]) + '\n')
+
+    for i in range(len(rawstack)):
+        datfile.write(imgnames[i][-21:] + '  ' + str(energies[i]))
+        if str(energies[i])[-2] == '.':
+            datfile.write('0')
+        datfile.write('   2.00\n')
+
+    datfile.close()
+
+    master.filedisp.set('Wrote stack file to ' + fname)
+
+def writetxt(master, is_i0 = False):
+
+    if is_i0:
+        fname = path.join(path.dirname(master.hdrfile), master.I0fname.get())
+        yvals = master.data.i0
+    else:
+        fname = path.join(path.dirname(master.hdrfile), master.spectrumfname.get())
+        yvals = master.data.od
+
+    energies = master.data.energies
+
+    outfile = open(fname, 'w')
+    outfile.write('% 1d\n')
+    outfile.write('% ' + fname[-16:-4] + '\n')
+    outfile.write('%  ' + str(len(yvals)) + '\n')
+    outfile.write('% from stack ' + (path.dirname(fname))[-12:] + '\n')
+    for i in range(len(yvals)):
+        outfile.write('\t' + str(energies[i]) + '\t' + str(yvals[i]) + '\n')
+    outfile.close()
+
+    if is_i0:
+        master.filedisp.set('Wrote I0 to ' + fname)
+    else:
+        master.filedisp.set('Wrote spectrum to ' + fname)
+
+def writealn(master):
+    fname = path.join(path.dirname(master.hdrfile), master.alnfname.get())
+
+    fout = open(fname, 'w')
+
+    fout.write('! Alignment file generated by STXM Live Analysis\n')
+    fout.write('! X-Y Pixel shifts after alignment\n')
+    fout.write('! Full images used\n')
+    fout.write('! Aligned to first image, ' + path.basename(master.data.imgfile[0]) + '  ' + str(master.data.energies[0]) + ' eV\n')
+    fout.write('! Correlation maximum determined by peak\n')
+    fout.write('! No edge enhancement\n')
+    fout.write('! Upsample factor 1000\n')
+    fout.write('! Gaussian smoothing of 3 pixels\n')
+    fout.write('ALIGN(0,0,0,0,1000,0.001,3,0,0,0,0,-1\n')
+    fout.write('PLOTIT(' + str(len(master.data.shifts)) + '\n')
+
+    for i in range(len(master.data.shifts)):
+        fout.write(path.basename(master.data.imgfile[i]) + '  ' + str(master.data.energies[i]) + '   ' + '2.00,')
+        fout.write(str(master.data.shifts[i][0]) + ',' + str(master.data.shifts[i][1]) + '\n')
+
+    master.filedisp.set('Wrote alignment file to ' + fname)
+    master.update_idletasks()
+
+    fout.close()