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Adding the option to uncompress the sessions folders
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Yasser Alemán Gómez committed May 25, 2024
1 parent 3659566 commit 71e8b71
Showing 1 changed file with 85 additions and 84 deletions.
169 changes: 85 additions & 84 deletions clabtoolkit/dicomtools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -337,12 +337,16 @@ def _create_session_series_names(dataset):

return ses_id, ser_id

def _uncompress_dicom_session(dic_dir: str, subj_ids=None):
def _uncompress_dicom_session(dic_dir: str,
boolrmtar: bool = False,
subj_ids=None):
"""
Uncompress session folders
@params:
dic_dir - Required : Directory containing the subjects. It assumes an organization in:
<subj_id>/<session_id>/<series_id>(Str)
boolrmtar - Optional : Boolean variable to remove the tar files after uncompressing the session. Default is False.
subj_ids - Optional : List of subject IDs to be considered. If not provided, it will consider all the subjects in the directory.
"""

if subj_ids is None:
Expand All @@ -362,48 +366,43 @@ def _uncompress_dicom_session(dic_dir: str, subj_ids=None):
elif not isinstance(subj_ids, list):
raise ValueError("The subj_ids parameter must be a list or a string")

n_subj = len(subj_ids)
# Failed sessions
fail_sess = []

# Loop around all the subjects
nsubj = len(subj_ids)
for i, subj_id in enumerate(subj_ids): # Loop along the IDs
subj_dir = os.path.join(dic_dir, subj_id)

cltmisc._printprogressbar(
i + 1,
nsubj,
"Processing subject "
+ subj_id
+ ": "
+ "("
+ str(i + 1)
+ "/"
+ str(nsubj)
+ ")",
)

# Loop along all the sessions inside the subject directory
for ses_tar in glob(
subj_dir + os.path.sep + "*.tar.gz"
): # Loop along the session
# print('SubjectId: ' + subjId + ' ======> Session: ' + sesId)
# Compress only if it is a folder
if os.path.isfile(ses_tar):
try:
# Compressing the folder
subprocess.run(
["tar", "xzf", ses_tar, "-C", subj_dir],
stdout=subprocess.PIPE,
universal_newlines=True,
)

# Removing the uncompressed dicom folder
# subprocess.run(
# ['rm', '-r', ses_tar], stdout=subprocess.PIPE, universal_newlines=True)

except:
fail_sess.append(ses_tar)
with Progress() as pb:
t1 = pb.add_task('[green]Compressing subjects...', total=n_subj)


# Loop around all the subjects
n_subj = len(subj_ids)
for i, subj_id in enumerate(subj_ids): # Loop along the IDs
subj_dir = os.path.join(dic_dir, subj_id)
pb.update(task_id=t1, description= f'[green]Uncompressing sessions for {subj_id} ({i+1}/{n_subj})', completed=i+1)

# Loop along all the sessions inside the subject directory
for ses_tar in glob(
subj_dir + os.path.sep + "*.tar.gz"
): # Loop along the session
# print('SubjectId: ' + subjId + ' ======> Session: ' + sesId)
# Compress only if it is a folder
if os.path.isfile(ses_tar):
try:
# Compressing the folder
subprocess.run(
["tar", "xzf", ses_tar, "-C", subj_dir],
stdout=subprocess.PIPE,
universal_newlines=True,
)

# Removing the uncompressed dicom folder
if boolrmtar:
subprocess.run(
['rm', '-r', ses_tar], stdout=subprocess.PIPE, universal_newlines=True)
except:
fail_sess.append(ses_tar)

pb.update(task_id=t1, description= f'[green]Compressing sessions for {subj_id} ({n_subj}/{n_subj})', completed=n_subj)

if fail_sess:
print("THE PROCESS FAILED TO UNCOMPRESS THE FOLLOWING TAR FILES:")
for i in fail_sess:
Expand Down Expand Up @@ -437,51 +436,53 @@ def _compress_dicom_session(dic_dir: str, subj_ids=None):
elif not isinstance(subj_ids, list):
raise ValueError("The subj_ids parameter must be a list or a string")

n_subj = len(subj_ids)
# Failed sessions
fail_sess = []

# Loop around all the subjects
nsubj = len(subj_ids)
for i, subj_id in enumerate(subj_ids): # Loop along the IDs
subj_dir = os.path.join(dic_dir, subj_id)

cltmisc._printprogressbar(
i + 1,
nsubj,
"Processing subject "
+ subj_id
+ ": "
+ "("
+ str(i + 1)
+ "/"
+ str(nsubj)
+ ")",
)

# Loop along all the sessions inside the subject directory
for ses_id in os.listdir(subj_dir): # Loop along the session
ses_dir = os.path.join(subj_dir, ses_id)
# print('SubjectId: ' + subjId + ' ======> Session: ' + sesId)
# Compress only if it is a folder
if os.path.isdir(ses_dir):
tar_filename = ses_dir + ".tar.gz"
try:
# Compressing the folder
subprocess.run(
["tar", "-C", subj_dir, "-czvf", tar_filename, ses_id],
stdout=subprocess.PIPE,
universal_newlines=True,
)

# Removing the uncompressed dicom folder
subprocess.run(
["rm", "-r", ses_dir],
stdout=subprocess.PIPE,
universal_newlines=True,
)

except:
fail_sess.append(ses_dir)
with Progress() as pb:
t1 = pb.add_task('[green]Compressing subjects...', total=n_subj)

# Loop around all the subjects
nsubj = len(subj_ids)
for i, subj_id in enumerate(subj_ids): # Loop along the IDs
subj_dir = os.path.join(dic_dir, subj_id)
pb.update(task_id=t1, description= f'[green]Compressing sessions for {subj_id} ({i+1}/{n_subj})', completed=i+1)

# Loop along all the sessions inside the subject directory
ses_dirs = os.listdir(subj_dir)

# Detect which of the folders are sessions
ses_dirs = [x for x in ses_dirs if os.path.isdir(os.path.join(subj_dir, x))]

# Detect which of the folders start with 'ses-'
ses_dirs = [x for x in ses_dirs if x.startswith('ses-')]
n_sessions = len(ses_dirs)

for n_ses, ses_id in enumerate(ses_dirs): # Loop along the session
ses_dir = os.path.join(subj_dir, ses_id)
# print('SubjectId: ' + subjId + ' ======> Session: ' + sesId)
# Compress only if it is a folder
if os.path.isdir(ses_dir):
tar_filename = ses_dir + ".tar.gz"
try:
# Compressing the folder
subprocess.run(
["tar", "-C", subj_dir, "-czvf", tar_filename, ses_id],
stdout=subprocess.PIPE,
universal_newlines=True,
)

# Removing the uncompressed dicom folder
subprocess.run(
["rm", "-r", ses_dir],
stdout=subprocess.PIPE,
universal_newlines=True,
)
except:
fail_sess.append(ses_dir)

pb.update(task_id=t1, description= f'[green]Compressing sessions for {subj_id} ({n_subj}/{n_subj})', completed=n_subj)

if fail_sess:
print("THE PROCESS FAILED TO COMPRESS THE FOLLOWING SESSIONS:")
for i in fail_sess:
Expand Down

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