def showDegCoh(filename, file_h5=None, rel_thresh=1e-4):
print(">>>>>>")
print("FILE: " + filename)
coor, coor_conj, mutual_intensity = loadNumpyFormatCoh(filename)
print("File Loaded")
if file_h5 is not None:
f = h5py.File(file_h5, 'w')
f["0_coor"] = coor
f["0_coor_conj"] = coor_conj
f["0_mutual_intensity"] = mutual_intensity
# f["0_mesh"] = [xStart, xEnd, xNpNew, yStart, yEnd, yNpNew]
#-----------------------------------------------------------
#FROM OLEG'S IGOR MACRO ------------------------------------
#-----------------------------------------------------------
nmInMutInt = ScaledMatrix(x_coord=coor,
y_coord=coor_conj,
z_values=mutual_intensity,
interpolator=True)
xStart = nmInMutInt.offset_x()
xNp = nmInMutInt.size_x()
xStep = nmInMutInt.delta_x()
xEnd = xStart + (xNp - 1) * xStep
yStart = nmInMutInt.offset_y()
yNp = nmInMutInt.size_y()
yStep = nmInMutInt.delta_y()
yEnd = yStart + (yNp - 1) * yStep
xNpNew = 2 * xNp - 1
yNpNew = 2 * yNp - 1
print("Creating Matrix wInMutCohRes")
wInMutCohRes = ScaledMatrix(x_coord=numpy.zeros(xNpNew),
y_coord=numpy.zeros(yNpNew),
z_values=numpy.zeros((xNpNew, yNpNew)),
interpolator=False)
xHalfNp = round(xNp * 0.5)
yHalfNp = round(yNp * 0.5)
wInMutCohRes.set_scale_from_steps(axis=0,
initial_scale_value=(xStart -
xHalfNp * xStep),
scale_step=xStep)
wInMutCohRes.set_scale_from_steps(axis=1,
initial_scale_value=(yStart -
yHalfNp * yStep),
scale_step=yStep)
dimx, dimy = wInMutCohRes.shape()
for inx in range(0, dimx):
for iny in range(0, dimy):
x = wInMutCohRes.get_x_value(inx)
y = wInMutCohRes.get_y_value(iny)
wInMutCohRes.set_z_value(
inx, iny,
nmInMutInt.interpolate_value(x, y) *
srwUtiNonZeroIntervB(x, xStart, xEnd) *
srwUtiNonZeroIntervB(y, yStart, yEnd))
wInMutCohRes.compute_interpolator()
print("Done")
if file_h5 is not None:
f["1_x"] = wInMutCohRes.get_x_values()
f["1_y"] = wInMutCohRes.get_y_values()
f["1_z"] = wInMutCohRes.get_z_values()
# f["1_mesh"] = [xStart, xEnd, xNpNew, yStart, yEnd, yNpNew]
print("Creating Matrix wMutCohNonRot")
wMutCohNonRot = ScaledMatrix(x_coord=nmInMutInt.get_x_values(),
y_coord=nmInMutInt.get_y_values(),
z_values=numpy.zeros(nmInMutInt.shape()),
interpolator=False)
abs_thresh = rel_thresh * abs(nmInMutInt.interpolate_value(0, 0))
dimx, dimy = wMutCohNonRot.shape()
for inx in range(0, dimx):
for iny in range(0, dimy):
x = wMutCohNonRot.get_x_value(inx)
y = wMutCohNonRot.get_y_value(iny)
wMutCohNonRot.set_z_value(
inx, iny,
numpy.abs(wInMutCohRes.interpolate_value(x, y)) / (numpy.sqrt(
abs(
wInMutCohRes.interpolate_value(x, x) *
wInMutCohRes.interpolate_value(y, y))) + abs_thresh))
wMutCohNonRot.compute_interpolator()
print("Done")
if file_h5 is not None:
f["2_x"] = wMutCohNonRot.get_x_values()
f["2_y"] = wMutCohNonRot.get_y_values()
f["2_z"] = wMutCohNonRot.get_z_values()
print("Creating Matrix nmResDegCoh")
nmResDegCoh = ScaledMatrix(x_coord=nmInMutInt.get_x_values(),
y_coord=nmInMutInt.get_y_values(),
z_values=numpy.zeros(nmInMutInt.shape()),
interpolator=False)
xmin = wMutCohNonRot.offset_x()
nx = wMutCohNonRot.size_x()
xstep = wMutCohNonRot.delta_x()
xmax = xmin + (nx - 1) * xstep
ymin = wMutCohNonRot.offset_y()
ny = wMutCohNonRot.size_y()
ystep = wMutCohNonRot.delta_y()
ymax = ymin + (ny - 1) * ystep
dimx, dimy = nmResDegCoh.shape()
for inx in range(0, dimx):
for iny in range(0, dimy):
x = nmResDegCoh.get_x_value(inx)
y = nmResDegCoh.get_y_value(iny)
nmResDegCoh.set_z_value(
inx, iny,
srwUtiInterp2DBilin((x + y), (x - y), wMutCohNonRot, xmin,
xmax, xstep, ymin, ymax, ystep))
print("Done: plotting Results")
if file_h5 is not None:
f["3_x"] = nmResDegCoh.get_x_values()
f["3_y"] = nmResDegCoh.get_y_values()
f["3_z"] = nmResDegCoh.get_z_values()
# f["3_mesh"] = [xmin, xmax, inx, ymin, ymax, iny]
f.close()
print("File %s written to disk." % file_h5)
if filename.endswith("1"):
xlabel = "(x1+x2)/2 [um]"
ylabel = "(x1-x2)/2 [um]"
else:
xlabel = "(y1+y2)/2 [um]"
ylabel = "(y1-y2)/2 [um]"
plot_scaled_matrix(nmResDegCoh, "nmResDegCoh", xlabel, ylabel)
def calculate_degree_of_coherence_vs_sum_and_difference_igor_macro(
coor, coor_conj, mutual_intensity, rel_thresh=1e-4):
nmInMutInt = ScaledMatrix(x_coord=coor,
y_coord=coor_conj,
z_values=mutual_intensity,
interpolator=True)
xStart = nmInMutInt.offset_x()
xNp = nmInMutInt.size_x()
xStep = nmInMutInt.delta_x()
xEnd = xStart + (xNp - 1) * xStep
yStart = nmInMutInt.offset_y()
yNp = nmInMutInt.size_y()
yStep = nmInMutInt.delta_y()
yEnd = yStart + (yNp - 1) * yStep
xNpNew = 2 * xNp - 1
yNpNew = 2 * yNp - 1
print("Creating Matrix wInMutCohRes")
wInMutCohRes = ScaledMatrix(x_coord=numpy.zeros(xNpNew),
y_coord=numpy.zeros(yNpNew),
z_values=numpy.zeros((xNpNew, yNpNew)),
interpolator=False)
xHalfNp = round(xNp * 0.5)
yHalfNp = round(yNp * 0.5)
wInMutCohRes.set_scale_from_steps(axis=0,
initial_scale_value=(xStart -
xHalfNp * xStep),
scale_step=xStep)
wInMutCohRes.set_scale_from_steps(axis=1,
initial_scale_value=(yStart -
yHalfNp * yStep),
scale_step=yStep)
dimx, dimy = wInMutCohRes.shape()
for inx in range(0, dimx):
for iny in range(0, dimy):
x = wInMutCohRes.get_x_value(inx)
y = wInMutCohRes.get_y_value(iny)
wInMutCohRes.set_z_value(
inx, iny,
nmInMutInt.interpolate_value(x, y) *
srwUtiNonZeroIntervB(x, xStart, xEnd) *
srwUtiNonZeroIntervB(y, yStart, yEnd))
wInMutCohRes.compute_interpolator()
print("Done")
print("Creating Matrix wMutCohNonRot")
wMutCohNonRot = ScaledMatrix(x_coord=nmInMutInt.get_x_values(),
y_coord=nmInMutInt.get_y_values(),
z_values=numpy.zeros(nmInMutInt.shape()),
interpolator=False)
abs_thresh = rel_thresh * abs(nmInMutInt.interpolate_value(0, 0))
dimx, dimy = wMutCohNonRot.shape()
for inx in range(0, dimx):
for iny in range(0, dimy):
x = wMutCohNonRot.get_x_value(inx)
y = wMutCohNonRot.get_y_value(iny)
wMutCohNonRot.set_z_value(
inx, iny,
numpy.abs(wInMutCohRes.interpolate_value(x, y)) / (numpy.sqrt(
abs(
wInMutCohRes.interpolate_value(x, x) *
wInMutCohRes.interpolate_value(y, y))) + abs_thresh))
wMutCohNonRot.compute_interpolator()
print("Done")
print("Creating Matrix nmResDegCoh")
nmResDegCoh = ScaledMatrix(x_coord=nmInMutInt.get_x_values(),
y_coord=nmInMutInt.get_y_values(),
z_values=numpy.zeros(nmInMutInt.shape()),
interpolator=False)
xmin = wMutCohNonRot.offset_x()
nx = wMutCohNonRot.size_x()
xstep = wMutCohNonRot.delta_x()
xmax = xmin + (nx - 1) * xstep
ymin = wMutCohNonRot.offset_y()
ny = wMutCohNonRot.size_y()
ystep = wMutCohNonRot.delta_y()
ymax = ymin + (ny - 1) * ystep
dimx, dimy = nmResDegCoh.shape()
for inx in range(0, dimx):
for iny in range(0, dimy):
x = nmResDegCoh.get_x_value(inx)
y = nmResDegCoh.get_y_value(iny)
nmResDegCoh.set_z_value(
inx, iny,
srwUtiInterp2DBilin((x + y), (x - y), wMutCohNonRot, xmin,
xmax, xstep, ymin, ymax, ystep))
return nmResDegCoh.get_x_values(), nmResDegCoh.get_y_values(
), nmResDegCoh.get_z_values()
