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Commit 00059c9a authored by Martin Genet's avatar Martin Genet
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Better mechanism to overwrite/keep temporary images in generate_images

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downsample_images.py
+ 17
− 7
View file @ 00059c9a
...@@ -31,6 +31,7 @@ def downsample_images( ...@@ -31,6 +31,7 @@ def downsample_images(
downsampling_factors, downsampling_factors,
images_ext="vti", images_ext="vti",
keep_resolution=0, keep_resolution=0,
overwrite_orig_images=1,
write_temp_images=0, write_temp_images=0,
verbose=0): verbose=0):
...@@ -185,7 +186,11 @@ def downsample_images( ...@@ -185,7 +186,11 @@ def downsample_images(
else: else:
rfft.SetInputData(image_downsampled) # MG20190520: Not sure why this does not work. rfft.SetInputData(image_downsampled) # MG20190520: Not sure why this does not work.
writer.SetInputConnection(rfft.GetOutputPort()) extract = vtk.vtkImageExtractComponents()
extract.SetInputConnection(rfft.GetOutputPort())
extract.SetComponents(0)
writer.SetInputConnection(extract.GetOutputPort())
if (keep_resolution): if (keep_resolution):
for k_frame in range(images_nframes): for k_frame in range(images_nframes):
...@@ -201,7 +206,7 @@ def downsample_images( ...@@ -201,7 +206,7 @@ def downsample_images(
writer_mul.SetFileName(images_folder+"/"+images_basename+"_mul"+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext) writer_mul.SetFileName(images_folder+"/"+images_basename+"_mul"+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext)
writer_mul.Write() writer_mul.Write()
writer.SetFileName(images_folder+"/"+images_basename+"_downsampled"+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext) writer.SetFileName(images_folder+"/"+images_basename+("_downsampled")*(not overwrite_orig_images)+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext)
writer.Write() writer.Write()
else: else:
for k_frame in range(images_nframes): for k_frame in range(images_nframes):
...@@ -255,11 +260,16 @@ def downsample_images( ...@@ -255,11 +260,16 @@ def downsample_images(
writer_sel.SetFileName(images_folder+"/"+images_basename+"_sel"+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext) writer_sel.SetFileName(images_folder+"/"+images_basename+"_sel"+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext)
writer_sel.Write() writer_sel.Write()
rfft = vtk.vtkImageRFFT() # MG20190520: Not sure why this is needed. rfft = vtk.vtkImageRFFT() # MG20190520: Not sure why this is needed.
rfft.SetDimensionality(images_ndim) # MG20190520: Not sure why this is needed. rfft.SetDimensionality(images_ndim) # MG20190520: Not sure why this is needed.
rfft.SetInputData(image_downsampled) # MG20190520: Not sure why this is needed. rfft.SetInputData(image_downsampled) # MG20190520: Not sure why this is needed.
rfft.Update() rfft.Update()
writer.SetInputData(rfft.GetOutput()) # MG20190520: Not sure why this is needed. extract = vtk.vtkImageExtractComponents() # MG20190520: Not sure why this is needed.
writer.SetFileName(images_folder+"/"+images_basename+"_downsampled"+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext) extract.SetInputData(rfft.GetOutput()) # MG20190520: Not sure why this is needed.
extract.SetComponents(0) # MG20190520: Not sure why this is needed.
extract.Update() # MG20190520: Not sure why this is needed.
writer.SetInputData(extract.GetOutput()) # MG20190520: Not sure why this is needed.
writer.SetFileName(images_folder+"/"+images_basename+("_downsampled")*(not overwrite_orig_images)+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext)
writer.Write() writer.Write()
generate_images.py
+ 20
− 15
View file @ 00059c9a
...@@ -62,7 +62,8 @@ def generate_images( ...@@ -62,7 +62,8 @@ def generate_images(
noise, noise,
deformation, deformation,
evolution, evolution,
generate_image_gradient=False, generate_image_gradient=0,
keep_temp_images=0,
verbose=0): verbose=0):
mypy.my_print(verbose, "*** generate_images ***") mypy.my_print(verbose, "*** generate_images ***")
...@@ -188,16 +189,18 @@ def generate_images( ...@@ -188,16 +189,18 @@ def generate_images(
images_basename=images["basename"], images_basename=images["basename"],
downsampling_factors=images["upsampling_factors"], downsampling_factors=images["upsampling_factors"],
keep_resolution=0, keep_resolution=0,
overwrite_orig_images=(not keep_temp_images),
write_temp_images=0, write_temp_images=0,
verbose=verbose) verbose=verbose)
for k_frame in range(images["n_frames"]): if (keep_temp_images):
os.rename( for k_frame in range(images["n_frames"]):
images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"], os.rename(
images["folder"]+"/"+images["basename"]+"_upsampled"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"]) images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"],
os.rename( images["folder"]+"/"+images["basename"]+"_upsampled"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"])
images["folder"]+"/"+images["basename"]+"_downsampled"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"], os.rename(
images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"]) images["folder"]+"/"+images["basename"]+"_downsampled"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"],
images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"])
if (images["data_type"] in ("float")): if (images["data_type"] in ("float")):
normalizing = False normalizing = False
...@@ -208,12 +211,14 @@ def generate_images( ...@@ -208,12 +211,14 @@ def generate_images(
images_folder=images["folder"], images_folder=images["folder"],
images_basename=images["basename"], images_basename=images["basename"],
images_datatype=images["data_type"], images_datatype=images["data_type"],
overwrite_orig_images=(not keep_temp_images),
verbose=verbose) verbose=verbose)
for k_frame in range(images["n_frames"]): if (keep_temp_images):
os.rename( for k_frame in range(images["n_frames"]):
src=images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"], os.rename(
dst=images["folder"]+"/"+images["basename"]+"_prenormalized"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"]) src=images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"],
os.rename( dst=images["folder"]+"/"+images["basename"]+"_prenormalized"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"])
src=images["folder"]+"/"+images["basename"]+"_normalized"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"], os.rename(
dst=images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"]) src=images["folder"]+"/"+images["basename"]+"_normalized"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"],
dst=images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"])
normalize_images.py
+ 2
− 1
View file @ 00059c9a
...@@ -30,6 +30,7 @@ def normalize_images( ...@@ -30,6 +30,7 @@ def normalize_images(
images_basename, images_basename,
images_datatype, images_datatype,
images_ext="vti", images_ext="vti",
overwrite_orig_images=1,
verbose=0): verbose=0):
mypy.my_print(verbose, "*** normalize_images ***") mypy.my_print(verbose, "*** normalize_images ***")
...@@ -94,5 +95,5 @@ def normalize_images( ...@@ -94,5 +95,5 @@ def normalize_images(
mypy.my_print(verbose, "k_frame = "+str(k_frame)) mypy.my_print(verbose, "k_frame = "+str(k_frame))
reader.SetFileName(images_folder+"/"+images_basename +"_"+str(k_frame).zfill(images_zfill)+"."+images_ext) reader.SetFileName(images_folder+"/"+images_basename +"_"+str(k_frame).zfill(images_zfill)+"."+images_ext)
writer.SetFileName(images_folder+"/"+images_basename+"_normalized"+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext) writer.SetFileName(images_folder+"/"+images_basename+("_normalized")*(not overwrite_orig_images)+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext)
writer.Write() writer.Write()
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