-                      rb2b36932
+                      r36d69e1
     """
     if data2d.data == None or data2d.x_bins == None or data2d.y_bins == None:
+    if data2d.data is None or data2d.x_bins is None or data2d.y_bins is None:
         raise ValueError, "Can't convert this data: data=None..."
     new_x = numpy.tile(data2d.x_bins, (len(data2d.y_bins), 1))
 …
     qy_data = new_y.flatten()
     q_data = numpy.sqrt(qx_data * qx_data + qy_data * qy_data)
     if data2d.err_data == None or numpy.any(data2d.err_data <= 0):
+    if data2d.err_data is None or numpy.any(data2d.err_data <= 0):
         new_err_data = numpy.sqrt(numpy.abs(new_data))
     else:

src/sas/sascalc/dataloader/readers/IgorReader.py

-                      rb699768
+                      r36d69e1
 #############################################################################
 import os
+import numpy
+import math
+#import logging
 from sas.sascalc.dataloader.data_info import Data2D
 from sas.sascalc.dataloader.data_info import Detector
 from sas.sascalc.dataloader.manipulations import reader2D_converter
+import numpy as np
 # Look for unit converter
 …
         """ Read file """
         if not os.path.isfile(filename):
+            raise ValueError, \
+            "Specified file %s is not a regular file" % filename
+        # Read file
+        f = open(filename, 'r')
+        buf = f.read()
+        # Instantiate data object
+            raise ValueError("Specified file %s is not a regular "
+                             "file" % filename)
         output = Data2D()
         output.filename = os.path.basename(filename)
         detector = Detector()
         if len(output.detector) > 0:
             print str(output.detector[0])
+        if len(output.detector):
+            print(str(output.detector[0]))
         output.detector.append(detector)
+        # Get content
+        dataStarted = False
+        lines = buf.split('\n')
+        itot = 0
+        x = []
+        y = []
+        ncounts = 0
+        xmin = None
+        xmax = None
+        ymin = None
+        ymax = None
+        i_x = 0
+        i_y = -1
+        i_tot_row = 0
+        isInfo = False
+        isCenter = False
+        data_conv_q = None
+        data_conv_i = None
+        if has_converter == True and output.Q_unit != '1/A':
+        data_conv_q = data_conv_i = None
+        if has_converter and output.Q_unit != '1/A':
             data_conv_q = Converter('1/A')
             # Test it
             data_conv_q(1.0, output.Q_unit)
         if has_converter == True and output.I_unit != '1/cm':
+        if has_converter and output.I_unit != '1/cm':
             data_conv_i = Converter('1/cm')
             # Test it
             data_conv_i(1.0, output.I_unit)
+        for line in lines:
+            # Find setup info line
+            if isInfo:
+                isInfo = False
+                line_toks = line.split()
+                # Wavelength in Angstrom
+                try:
+                    wavelength = float(line_toks[1])
+                except:
+                    msg = "IgorReader: can't read this file, missing wavelength"
+                    raise ValueError, msg
+            #Find # of bins in a row assuming the detector is square.
+            if dataStarted == True:
+                try:
+                    value = float(line)
+                except:
+                    # Found a non-float entry, skip it
+                    continue
+                # Get total bin number
+            i_tot_row += 1
+        i_tot_row = math.ceil(math.sqrt(i_tot_row)) - 1
+        #print "i_tot", i_tot_row
+        size_x = i_tot_row  # 192#128
+        size_y = i_tot_row  # 192#128
+        output.data = numpy.zeros([size_x, size_y])
+        output.err_data = numpy.zeros([size_x, size_y])
+        #Read Header and 2D data
+        for line in lines:
+            # Find setup info line
+            if isInfo:
+                isInfo = False
+                line_toks = line.split()
+                # Wavelength in Angstrom
+                try:
+                    wavelength = float(line_toks[1])
+                except:
+                    msg = "IgorReader: can't read this file, missing wavelength"
+                    raise ValueError, msg
+                # Distance in meters
+                try:
+                    distance = float(line_toks[3])
+                except:
+                    msg = "IgorReader: can't read this file, missing distance"
+                    raise ValueError, msg
+                # Distance in meters
+                try:
+                    transmission = float(line_toks[4])
+                except:
+                    msg = "IgorReader: can't read this file, "
+                    msg += "missing transmission"
+                    raise ValueError, msg
+            if line.count("LAMBDA") > 0:
+                isInfo = True
+            # Find center info line
+            if isCenter:
+                isCenter = False
+                line_toks = line.split()
+                # Center in bin number: Must substrate 1 because
+                #the index starts from 1
+                center_x = float(line_toks[0]) - 1
+                center_y = float(line_toks[1]) - 1
+            if line.count("BCENT") > 0:
+                isCenter = True
+            # Find data start
+            if line.count("***")>0:
+                dataStarted = True
+                # Check that we have all the info
+                if wavelength == None \
+                    or distance == None \
+                    or center_x == None \
+                    or center_y == None:
+                    msg = "IgorReader:Missing information in data file"
+                    raise ValueError, msg
+            if dataStarted == True:
+                try:
+                    value = float(line)
+                except:
+                    # Found a non-float entry, skip it
+                    continue
+                # Get bin number
+                if math.fmod(itot, i_tot_row) == 0:
+                    i_x = 0
+                    i_y += 1
+                else:
+                    i_x += 1
+                output.data[i_y][i_x] = value
+                ncounts += 1
+                # Det 640 x 640 mm
+                # Q = 4pi/lambda sin(theta/2)
+                # Bin size is 0.5 cm
+                #REmoved +1 from theta = (i_x-center_x+1)*0.5 / distance
+                # / 100.0 and
+                #REmoved +1 from theta = (i_y-center_y+1)*0.5 /
+                # distance / 100.0
+                #ToDo: Need  complete check if the following
+                # covert process is consistent with fitting.py.
+                theta = (i_x - center_x) * 0.5 / distance / 100.0
+                qx = 4.0 * math.pi / wavelength * math.sin(theta/2.0)
+                if has_converter == True and output.Q_unit != '1/A':
+                    qx = data_conv_q(qx, units=output.Q_unit)
+                if xmin == None or qx < xmin:
+                    xmin = qx
+                if xmax == None or qx > xmax:
+                    xmax = qx
+                theta = (i_y - center_y) * 0.5 / distance / 100.0
+                qy = 4.0 * math.pi / wavelength * math.sin(theta / 2.0)
+                if has_converter == True and output.Q_unit != '1/A':
+                    qy = data_conv_q(qy, units=output.Q_unit)
+                if ymin == None or qy < ymin:
+                    ymin = qy
+                if ymax == None or qy > ymax:
+                    ymax = qy
+                if not qx in x:
+                    x.append(qx)
+                if not qy in y:
+                    y.append(qy)
+                itot += 1
+        data_row = 0
+        wavelength = distance = center_x = center_y = None
+        dataStarted = isInfo = isCenter = False
+        with open(filename, 'r') as f:
+            for line in f:
+                data_row += 1
+                # Find setup info line
+                if isInfo:
+                    isInfo = False
+                    line_toks = line.split()
+                    # Wavelength in Angstrom
+                    try:
+                        wavelength = float(line_toks[1])
+                    except ValueError:
+                        msg = "IgorReader: can't read this file, missing wavelength"
+                        raise ValueError(msg)
+                    # Distance in meters
+                    try:
+                        distance = float(line_toks[3])
+                    except ValueError:
+                        msg = "IgorReader: can't read this file, missing distance"
+                        raise ValueError(msg)
+                    # Distance in meters
+                    try:
+                        transmission = float(line_toks[4])
+                    except:
+                        msg = "IgorReader: can't read this file, "
+                        msg += "missing transmission"
+                        raise ValueError(msg)
+                if line.count("LAMBDA"):
+                    isInfo = True
+                # Find center info line
+                if isCenter:
+                    isCenter = False
+                    line_toks = line.split()
+                    # Center in bin number: Must subtract 1 because
+                    # the index starts from 1
+                    center_x = float(line_toks[0]) - 1
+                    center_y = float(line_toks[1]) - 1
+                if line.count("BCENT"):
+                    isCenter = True
+                # Find data start
+                if line.count("***"):
+                    # now have to continue to blank line
+                    dataStarted = True
+                    # Check that we have all the info
+                    if (wavelength is None
+                            or distance is None
+                            or center_x is None
+                            or center_y is None):
+                        msg = "IgorReader:Missing information in data file"
+                        raise ValueError(msg)
+                if dataStarted:
+                    if len(line.rstrip()):
+                        continue
+                    else:
+                        break
+        # The data is loaded in row major order (last index changing most
+        # rapidly). However, the original data is in column major order (first
+        # index changing most rapidly). The swap to column major order is done
+        # in reader2D_converter at the end of this method.
+        data = np.loadtxt(filename, skiprows=data_row)
+        size_x = size_y = int(np.rint(np.sqrt(data.size)))
+        output.data = np.reshape(data, (size_x, size_y))
+        output.err_data = np.zeros_like(output.data)
+        # Det 640 x 640 mm
+        # Q = 4 * pi/lambda * sin(theta/2)
+        # Bin size is 0.5 cm
+        # Removed +1 from theta = (i_x - center_x + 1)*0.5 / distance
+        # / 100.0 and
+        # Removed +1 from theta = (i_y - center_y + 1)*0.5 /
+        # distance / 100.0
+        # ToDo: Need  complete check if the following
+        # convert process is consistent with fitting.py.
+        # calculate qx, qy bin centers of each pixel in the image
+        theta = (np.arange(size_x) - center_x) * 0.5 / distance / 100.
+        qx = 4 * np.pi / wavelength * np.sin(theta/2)
+        theta = (np.arange(size_y) - center_y) * 0.5 / distance / 100.
+        qy = 4 * np.pi / wavelength * np.sin(theta/2)
+        if has_converter and output.Q_unit != '1/A':
+            qx = data_conv_q(qx, units=output.Q_unit)
+            qy = data_conv_q(qx, units=output.Q_unit)
+        xmax = np.max(qx)
+        xmin = np.min(qx)
+        ymax = np.max(qy)
+        ymin = np.min(qy)
+        # calculate edge offset in q.
         theta = 0.25 / distance / 100.0
         xstep = 4.0 * math.pi / wavelength * math.sin(theta / 2.0)
+        xstep = 4.0 * np.pi / wavelength * np.sin(theta / 2.0)
         theta = 0.25 / distance / 100.0
         ystep = 4.0 * math.pi/ wavelength * math.sin(theta / 2.0)
+        ystep = 4.0 * np.pi/ wavelength * np.sin(theta / 2.0)
         # Store all data ######################################
         # Store wavelength
         if has_converter == True and output.source.wavelength_unit != 'A':
+        if has_converter and output.source.wavelength_unit != 'A':
             conv = Converter('A')
             wavelength = conv(wavelength, units=output.source.wavelength_unit)
 …
         # Store distance
         if has_converter == True and detector.distance_unit != 'm':
+        if has_converter and detector.distance_unit != 'm':
             conv = Converter('m')
             distance = conv(distance, units=detector.distance_unit)
 …
         output.sample.transmission = transmission
         # Store pixel size
+        # Store pixel size (mm)
         pixel = 5.0
         if has_converter == True and detector.pixel_size_unit != 'mm':
+        if has_converter and detector.pixel_size_unit != 'mm':
             conv = Converter('mm')
             pixel = conv(pixel, units=detector.pixel_size_unit)
 …
         # Store limits of the image (2D array)
         xmin = xmin - xstep / 2.0
         xmax = xmax + xstep / 2.0
         ymin = ymin - ystep / 2.0
         ymax = ymax + ystep / 2.0
         if has_converter == True and output.Q_unit != '1/A':
+        xmin -= xstep / 2.0
+        xmax += xstep / 2.0
+        ymin -= ystep / 2.0
+        ymax += ystep / 2.0
+        if has_converter and output.Q_unit != '1/A':
             xmin = data_conv_q(xmin, units=output.Q_unit)
             xmax = data_conv_q(xmax, units=output.Q_unit)
 …
         # Store x and y axis bin centers
         output.x_bins = x
         output.y_bins = y
+        output.x_bins = qx.tolist()
+        output.y_bins = qy.tolist()
         # Units

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SasView

Changeset 36d69e1 in sasview for src/sas

Legend:

src/sas/sascalc/dataloader/manipulations.py

src/sas/sascalc/dataloader/readers/IgorReader.py

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