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Check for pixel spacing between two folder images
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5
down vote
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Im trying to match the pixel spacing between two folders, here matches has 994 keys and it shows that i may take more than a day to compute this. Is there any way i can speed up this operation.
the load series function looks like this
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
import csv
bar = ProgressBar()
file = open('BenignTest.csv', 'w')
writer = csv.writer(file)
for item in bar(matches.keys()):
for case in matches[item]:
load_case = load_series(case)
if load_case.GetSpacing() == load_series(item).GetSpacing():
writer.writerow((item , case))
break
The matches dictionary looks like this,
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': ['/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354']...........
Thanks in advance
python performance
asked Aug 14 at 7:38
Ryan
1284
add a comment |Â
up vote
5
down vote
favorite
Im trying to match the pixel spacing between two folders, here matches has 994 keys and it shows that i may take more than a day to compute this. Is there any way i can speed up this operation.
the load series function looks like this
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
import csv
bar = ProgressBar()
file = open('BenignTest.csv', 'w')
writer = csv.writer(file)
for item in bar(matches.keys()):
for case in matches[item]:
load_case = load_series(case)
if load_case.GetSpacing() == load_series(item).GetSpacing():
writer.writerow((item , case))
break
The matches dictionary looks like this,
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': ['/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354']...........
Thanks in advance
python performance
asked Aug 14 at 7:38
Ryan
1284
1
Cross-posted from Stack Overflow
– Mathias Ettinger
Aug 14 at 8:02
add a comment |Â
up vote
5
down vote
favorite
up vote
5
down vote
favorite
Im trying to match the pixel spacing between two folders, here matches has 994 keys and it shows that i may take more than a day to compute this. Is there any way i can speed up this operation.
the load series function looks like this
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
import csv
bar = ProgressBar()
file = open('BenignTest.csv', 'w')
writer = csv.writer(file)
for item in bar(matches.keys()):
for case in matches[item]:
load_case = load_series(case)
if load_case.GetSpacing() == load_series(item).GetSpacing():
writer.writerow((item , case))
break
The matches dictionary looks like this,
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': ['/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354']...........
Thanks in advance
python performance
asked Aug 14 at 7:38
Ryan
1284
Im trying to match the pixel spacing between two folders, here matches has 994 keys and it shows that i may take more than a day to compute this. Is there any way i can speed up this operation.
the load series function looks like this
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
import csv
bar = ProgressBar()
file = open('BenignTest.csv', 'w')
writer = csv.writer(file)
for item in bar(matches.keys()):
for case in matches[item]:
load_case = load_series(case)
if load_case.GetSpacing() == load_series(item).GetSpacing():
writer.writerow((item , case))
break
The matches dictionary looks like this,
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': ['/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354']...........
Thanks in advance
python performance
asked Aug 14 at 7:38
Ryan
1284
edited Aug 14 at 8:37
asked Aug 14 at 7:38
Ryan
1284
asked Aug 14 at 7:38
Ryan
1284
asked Aug 14 at 7:38
Ryan
1284
1284
1
Cross-posted from Stack Overflow
– Mathias Ettinger
Aug 14 at 8:02
add a comment |Â
1
Cross-posted from Stack Overflow
– Mathias Ettinger
Aug 14 at 8:02
1
1
Cross-posted from Stack Overflow
– Mathias Ettinger
Aug 14 at 8:02
Cross-posted from Stack Overflow
– Mathias Ettinger
Aug 14 at 8:02
add a comment |Â
2 Answers
2
active
oldest
votes
up vote
4
down vote
accepted
The simplest improvement that you can do right now is to avoid recomputing the same reference image over and over for each case of an item: just store load_series(item).GetSpacing() before looping over each case.
You can also use writer.writerows and feed it a list or a generator instead of writer.writerow. This should optimize disk writes a bit, even though reading images should be the task that take up the most resources here.
Proposed improvements:
import csv
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
def generate_equal_spacing(matches, progress_bar=None):
items = matches.keys()
if progress_bar is not None:
items = progress_bar(items)
for item in items:
reference_spacing = load_series(item).GetSpacing()
for case in matches[item]:
if load_series(case).GetSpacing() == reference_spacing:
yield (item, case)
break
def main(matches, output_filename='BenignTest.csv'):
with open(output_filename, 'w') as f:
writer = csv.writer(f)
writer.writerows(generate_equal_spacing(matches, ProgressBar()))
if __name__ == '__main__':
main(
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': [
'/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354',
],
...
)
answered Aug 14 at 8:43
Mathias Ettinger
22k32876
2
In addition:functools.lru_cachemay increase performance further if a lot of the files are the same.
– Peilonrayz
Aug 14 at 8:51
add a comment |Â
up vote
2
down vote
If you just want each image's spacing information, you don't actually need to read the images, just the header info.
Here is a SimpleITK example showing how to read an image's meta-data information without loading the pixels.
https://simpleitk.readthedocs.io/en/latest/Examples/DicomImagePrintTags/Documentation.html
So change your load_series function something like this:
def load_series_spacing(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
reader.ReadImageInformation();
return reader.GetSpacing()
And then, of course, adjust the comparisons in the main routine accordingly, since we're returning spacing, not the actual images.
answered Aug 17 at 14:13
Dave Chen
214
Hi Dave, Thanks for your inputs, But when i run your function, i get thisAttributeError: 'ImageSeriesReader' object has no attribute 'ReadImageInformation'any ideas on this ?
– Ryan
Aug 20 at 8:51
Oops, my bad. The method ReadImageInformation is in the class ImageFileReader, not ImageSeriesReader. So you can get the header info for each individual slice. Then GetSpacing would return the X-Y pixel spacing. If you want the Z spacing, you'll have to do some math from the Origins of neighboring slices.
– Dave Chen
Aug 20 at 14:33
add a comment |Â
2 Answers
2
active
oldest
votes
2 Answers
2
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
4
down vote
accepted
The simplest improvement that you can do right now is to avoid recomputing the same reference image over and over for each case of an item: just store load_series(item).GetSpacing() before looping over each case.
You can also use writer.writerows and feed it a list or a generator instead of writer.writerow. This should optimize disk writes a bit, even though reading images should be the task that take up the most resources here.
Proposed improvements:
import csv
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
def generate_equal_spacing(matches, progress_bar=None):
items = matches.keys()
if progress_bar is not None:
items = progress_bar(items)
for item in items:
reference_spacing = load_series(item).GetSpacing()
for case in matches[item]:
if load_series(case).GetSpacing() == reference_spacing:
yield (item, case)
break
def main(matches, output_filename='BenignTest.csv'):
with open(output_filename, 'w') as f:
writer = csv.writer(f)
writer.writerows(generate_equal_spacing(matches, ProgressBar()))
if __name__ == '__main__':
main(
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': [
'/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354',
],
...
)
answered Aug 14 at 8:43
Mathias Ettinger
22k32876
2
In addition:functools.lru_cachemay increase performance further if a lot of the files are the same.
– Peilonrayz
Aug 14 at 8:51
add a comment |Â
up vote
4
down vote
accepted
The simplest improvement that you can do right now is to avoid recomputing the same reference image over and over for each case of an item: just store load_series(item).GetSpacing() before looping over each case.
You can also use writer.writerows and feed it a list or a generator instead of writer.writerow. This should optimize disk writes a bit, even though reading images should be the task that take up the most resources here.
Proposed improvements:
import csv
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
def generate_equal_spacing(matches, progress_bar=None):
items = matches.keys()
if progress_bar is not None:
items = progress_bar(items)
for item in items:
reference_spacing = load_series(item).GetSpacing()
for case in matches[item]:
if load_series(case).GetSpacing() == reference_spacing:
yield (item, case)
break
def main(matches, output_filename='BenignTest.csv'):
with open(output_filename, 'w') as f:
writer = csv.writer(f)
writer.writerows(generate_equal_spacing(matches, ProgressBar()))
if __name__ == '__main__':
main(
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': [
'/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354',
],
...
)
answered Aug 14 at 8:43
Mathias Ettinger
22k32876
2
In addition:functools.lru_cachemay increase performance further if a lot of the files are the same.
– Peilonrayz
Aug 14 at 8:51
add a comment |Â
up vote
4
down vote
accepted
up vote
4
down vote
accepted
The simplest improvement that you can do right now is to avoid recomputing the same reference image over and over for each case of an item: just store load_series(item).GetSpacing() before looping over each case.
You can also use writer.writerows and feed it a list or a generator instead of writer.writerow. This should optimize disk writes a bit, even though reading images should be the task that take up the most resources here.
Proposed improvements:
import csv
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
def generate_equal_spacing(matches, progress_bar=None):
items = matches.keys()
if progress_bar is not None:
items = progress_bar(items)
for item in items:
reference_spacing = load_series(item).GetSpacing()
for case in matches[item]:
if load_series(case).GetSpacing() == reference_spacing:
yield (item, case)
break
def main(matches, output_filename='BenignTest.csv'):
with open(output_filename, 'w') as f:
writer = csv.writer(f)
writer.writerows(generate_equal_spacing(matches, ProgressBar()))
if __name__ == '__main__':
main(
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': [
'/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354',
],
...
)
answered Aug 14 at 8:43
Mathias Ettinger
22k32876
The simplest improvement that you can do right now is to avoid recomputing the same reference image over and over for each case of an item: just store load_series(item).GetSpacing() before looping over each case.
You can also use writer.writerows and feed it a list or a generator instead of writer.writerow. This should optimize disk writes a bit, even though reading images should be the task that take up the most resources here.
Proposed improvements:
import csv
import SimpleITK as sitk
def load_series(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
return reader.Execute()
def generate_equal_spacing(matches, progress_bar=None):
items = matches.keys()
if progress_bar is not None:
items = progress_bar(items)
for item in items:
reference_spacing = load_series(item).GetSpacing()
for case in matches[item]:
if load_series(case).GetSpacing() == reference_spacing:
yield (item, case)
break
def main(matches, output_filename='BenignTest.csv'):
with open(output_filename, 'w') as f:
writer = csv.writer(f)
writer.writerows(generate_equal_spacing(matches, ProgressBar()))
if __name__ == '__main__':
main(
'/mnt/sdd1/DSB2017/stage1/0030a160d58723ff36d73f41b170ec21': [
'/mnt/sde1/Cancer/128443/01-02-1999-LSS-59120/2-0OPAGELSPLUSD3602.512060.00.11.5-98506',
'/mnt/sde1/Cancer/213485/01-02-1999-ACRIN-13247/3-0OPAGELSPLUSLUNG3502.51204026.71.5-85097',
'/mnt/sde1/Cancer/206342/01-02-1999-ACRIN-68321/3-0OPAGELSPLUSLUNG3702.51205033.31.5-72233',
'/mnt/sde1/Cancer/200209/01-02-2000-CRIN-10216/3-1OPAGELSPLUSLUNG4002.51204026.71.5-42354',
],
...
)
answered Aug 14 at 8:43
Mathias Ettinger
22k32876
answered Aug 14 at 8:43
Mathias Ettinger
22k32876
answered Aug 14 at 8:43
Mathias Ettinger
22k32876
answered Aug 14 at 8:43
Mathias Ettinger
22k32876
22k32876
2
In addition:functools.lru_cachemay increase performance further if a lot of the files are the same.
– Peilonrayz
Aug 14 at 8:51
add a comment |Â
2
In addition:functools.lru_cachemay increase performance further if a lot of the files are the same.
– Peilonrayz
Aug 14 at 8:51
2
2
In addition:
functools.lru_cache may increase performance further if a lot of the files are the same.– Peilonrayz
Aug 14 at 8:51
In addition:
functools.lru_cache may increase performance further if a lot of the files are the same.– Peilonrayz
Aug 14 at 8:51
add a comment |Â
up vote
2
down vote
If you just want each image's spacing information, you don't actually need to read the images, just the header info.
Here is a SimpleITK example showing how to read an image's meta-data information without loading the pixels.
https://simpleitk.readthedocs.io/en/latest/Examples/DicomImagePrintTags/Documentation.html
So change your load_series function something like this:
def load_series_spacing(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
reader.ReadImageInformation();
return reader.GetSpacing()
And then, of course, adjust the comparisons in the main routine accordingly, since we're returning spacing, not the actual images.
answered Aug 17 at 14:13
Dave Chen
214
Hi Dave, Thanks for your inputs, But when i run your function, i get thisAttributeError: 'ImageSeriesReader' object has no attribute 'ReadImageInformation'any ideas on this ?
– Ryan
Aug 20 at 8:51
Oops, my bad. The method ReadImageInformation is in the class ImageFileReader, not ImageSeriesReader. So you can get the header info for each individual slice. Then GetSpacing would return the X-Y pixel spacing. If you want the Z spacing, you'll have to do some math from the Origins of neighboring slices.
– Dave Chen
Aug 20 at 14:33
add a comment |Â
up vote
2
down vote
If you just want each image's spacing information, you don't actually need to read the images, just the header info.
Here is a SimpleITK example showing how to read an image's meta-data information without loading the pixels.
https://simpleitk.readthedocs.io/en/latest/Examples/DicomImagePrintTags/Documentation.html
So change your load_series function something like this:
def load_series_spacing(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
reader.ReadImageInformation();
return reader.GetSpacing()
And then, of course, adjust the comparisons in the main routine accordingly, since we're returning spacing, not the actual images.
answered Aug 17 at 14:13
Dave Chen
214
Hi Dave, Thanks for your inputs, But when i run your function, i get thisAttributeError: 'ImageSeriesReader' object has no attribute 'ReadImageInformation'any ideas on this ?
– Ryan
Aug 20 at 8:51
Oops, my bad. The method ReadImageInformation is in the class ImageFileReader, not ImageSeriesReader. So you can get the header info for each individual slice. Then GetSpacing would return the X-Y pixel spacing. If you want the Z spacing, you'll have to do some math from the Origins of neighboring slices.
– Dave Chen
Aug 20 at 14:33
add a comment |Â
up vote
2
down vote
up vote
2
down vote
If you just want each image's spacing information, you don't actually need to read the images, just the header info.
Here is a SimpleITK example showing how to read an image's meta-data information without loading the pixels.
https://simpleitk.readthedocs.io/en/latest/Examples/DicomImagePrintTags/Documentation.html
So change your load_series function something like this:
def load_series_spacing(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
reader.ReadImageInformation();
return reader.GetSpacing()
And then, of course, adjust the comparisons in the main routine accordingly, since we're returning spacing, not the actual images.
answered Aug 17 at 14:13
Dave Chen
214
If you just want each image's spacing information, you don't actually need to read the images, just the header info.
Here is a SimpleITK example showing how to read an image's meta-data information without loading the pixels.
https://simpleitk.readthedocs.io/en/latest/Examples/DicomImagePrintTags/Documentation.html
So change your load_series function something like this:
def load_series_spacing(path):
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(path)
reader.SetFileNames(dicom_names)
reader.ReadImageInformation();
return reader.GetSpacing()
And then, of course, adjust the comparisons in the main routine accordingly, since we're returning spacing, not the actual images.
answered Aug 17 at 14:13
Dave Chen
214
answered Aug 17 at 14:13
Dave Chen
214
answered Aug 17 at 14:13
Dave Chen
214
answered Aug 17 at 14:13
Dave Chen
214
214
Hi Dave, Thanks for your inputs, But when i run your function, i get thisAttributeError: 'ImageSeriesReader' object has no attribute 'ReadImageInformation'any ideas on this ?
– Ryan
Aug 20 at 8:51
Oops, my bad. The method ReadImageInformation is in the class ImageFileReader, not ImageSeriesReader. So you can get the header info for each individual slice. Then GetSpacing would return the X-Y pixel spacing. If you want the Z spacing, you'll have to do some math from the Origins of neighboring slices.
– Dave Chen
Aug 20 at 14:33
add a comment |Â
Hi Dave, Thanks for your inputs, But when i run your function, i get thisAttributeError: 'ImageSeriesReader' object has no attribute 'ReadImageInformation'any ideas on this ?
– Ryan
Aug 20 at 8:51
Oops, my bad. The method ReadImageInformation is in the class ImageFileReader, not ImageSeriesReader. So you can get the header info for each individual slice. Then GetSpacing would return the X-Y pixel spacing. If you want the Z spacing, you'll have to do some math from the Origins of neighboring slices.
– Dave Chen
Aug 20 at 14:33
Hi Dave, Thanks for your inputs, But when i run your function, i get this
AttributeError: 'ImageSeriesReader' object has no attribute 'ReadImageInformation' any ideas on this ?– Ryan
Aug 20 at 8:51
Hi Dave, Thanks for your inputs, But when i run your function, i get this
AttributeError: 'ImageSeriesReader' object has no attribute 'ReadImageInformation' any ideas on this ?– Ryan
Aug 20 at 8:51
Oops, my bad. The method ReadImageInformation is in the class ImageFileReader, not ImageSeriesReader. So you can get the header info for each individual slice. Then GetSpacing would return the X-Y pixel spacing. If you want the Z spacing, you'll have to do some math from the Origins of neighboring slices.
– Dave Chen
Aug 20 at 14:33
Oops, my bad. The method ReadImageInformation is in the class ImageFileReader, not ImageSeriesReader. So you can get the header info for each individual slice. Then GetSpacing would return the X-Y pixel spacing. If you want the Z spacing, you'll have to do some math from the Origins of neighboring slices.
– Dave Chen
Aug 20 at 14:33
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Cross-posted from Stack Overflow
– Mathias Ettinger
Aug 14 at 8:02