diff --git a/downsample_images.py b/downsample_images.py
index 4031a70aeadea4693b3a857e1ef2eff378c7b857..41f0ea20c84027aaf8413167e188f2467c738433 100644
--- a/downsample_images.py
+++ b/downsample_images.py
@@ -31,6 +31,7 @@ def downsample_images(
downsampling_factors,
images_ext="vti",
keep_resolution=0,
+ overwrite_orig_images=1,
write_temp_images=0,
verbose=0):
@@ -185,7 +186,11 @@ def downsample_images(
else:
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):
for k_frame in range(images_nframes):
@@ -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.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()
else:
for k_frame in range(images_nframes):
@@ -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.Write()
- rfft = vtk.vtkImageRFFT() # 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 = vtk.vtkImageRFFT() # 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.Update()
- writer.SetInputData(rfft.GetOutput()) # MG20190520: Not sure why this is needed.
- writer.SetFileName(images_folder+"/"+images_basename+"_downsampled"+"_"+str(k_frame).zfill(images_zfill)+"."+images_ext)
+ extract = vtk.vtkImageExtractComponents() # MG20190520: Not sure why this is needed.
+ 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()
diff --git a/generate_images.py b/generate_images.py
index 2cf9491aeb20a9abc362fea3d87903edba7fcdce..cbc4260b9e55d5c3d51ebb8b65675c74a6baba24 100644
--- a/generate_images.py
+++ b/generate_images.py
@@ -62,7 +62,8 @@ def generate_images(
noise,
deformation,
evolution,
- generate_image_gradient=False,
+ generate_image_gradient=0,
+ keep_temp_images=0,
verbose=0):
mypy.my_print(verbose, "*** generate_images ***")
@@ -188,16 +189,18 @@ def generate_images(
images_basename=images["basename"],
downsampling_factors=images["upsampling_factors"],
keep_resolution=0,
+ overwrite_orig_images=(not keep_temp_images),
write_temp_images=0,
verbose=verbose)
- for k_frame in range(images["n_frames"]):
- os.rename(
- images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"],
- images["folder"]+"/"+images["basename"]+"_upsampled"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"])
- os.rename(
- 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 (keep_temp_images):
+ for k_frame in range(images["n_frames"]):
+ os.rename(
+ images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"],
+ images["folder"]+"/"+images["basename"]+"_upsampled"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"])
+ os.rename(
+ 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")):
normalizing = False
@@ -208,12 +211,14 @@ def generate_images(
images_folder=images["folder"],
images_basename=images["basename"],
images_datatype=images["data_type"],
+ overwrite_orig_images=(not keep_temp_images),
verbose=verbose)
- for k_frame in range(images["n_frames"]):
- os.rename(
- src=images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"],
- dst=images["folder"]+"/"+images["basename"]+"_prenormalized"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"])
- os.rename(
- 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"])
+ if (keep_temp_images):
+ for k_frame in range(images["n_frames"]):
+ os.rename(
+ src=images["folder"]+"/"+images["basename"]+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"],
+ dst=images["folder"]+"/"+images["basename"]+"_prenormalized"+"_"+str(k_frame).zfill(images["zfill"])+"."+images["ext"])
+ os.rename(
+ 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"])
diff --git a/normalize_images.py b/normalize_images.py
index e292458d7a7fb0b5fc689fa516ffc5f15a094afe..d2b1c827f520a6f15f4fe2f91dca9ce887566382 100644
--- a/normalize_images.py
+++ b/normalize_images.py
@@ -30,6 +30,7 @@ def normalize_images(
images_basename,
images_datatype,
images_ext="vti",
+ overwrite_orig_images=1,
verbose=0):
mypy.my_print(verbose, "*** normalize_images ***")
@@ -94,5 +95,5 @@ def normalize_images(
mypy.my_print(verbose, "k_frame = "+str(k_frame))
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()