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Rcq updates9 #473

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merged 2 commits into from
Jul 21, 2024
Merged

Rcq updates9 #473

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7ea7d82
Update processors_v3.py
bud42 Jul 17, 2024
be45931
keep_multis in analysis
bud42 Jul 21, 2024
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32 changes: 32 additions & 0 deletions dax/processors_v3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1407,6 +1407,7 @@ def is_first_mr_session(self, session, project_data):
def _map_inputs(self, session, project_data):
inputs = self.proc_inputs
artefacts_by_input = {k: [] for k in inputs}
artefact_ids_by_input = {k: [] for k in inputs}

# Get lists for scans/assrs for this session
LOGGER.debug('prepping session data')
Expand Down Expand Up @@ -1468,8 +1469,39 @@ def _map_inputs(self, session, project_data):
# Break if the scan matches so we don't find it again comparing
# vs a different requested type
artefacts_by_input[i].append(cscan['full_path'])
artefact_ids_by_input[i].append(scanid)
break

# If requested, check for multiple matching scans in the list and only keep
# the first. Sort lowercase by alpha, on scan ID.
if len(artefacts_by_input[i]) > 0 and iv['keep_multis'] != 'all':
scan_info = zip(
artefacts_by_input[i],
artefact_ids_by_input[i],
)
sorted_info = sorted(scan_info, key=lambda x: str(x[1]).lower())
num_scans = sum(1 for _ in sorted_info)
if iv['keep_multis'] == 'first':
idx_multi = 1
elif iv['keep_multis'] == 'last':
idx_multi = num_scans
else:
try:
idx_multi = int(iv['keep_multis'])
except:
msg = f'For {i}, keep_multis must be first, last, or index 1,2,3,...'
LOGGER.error(msg)
raise AutoProcessorError(msg)
if idx_multi > num_scans:
msg = f'Requested {idx_multi}th scan for {i}, but only {num_scans} found'
LOGGER.error(msg)
raise AutoProcessorError(msg)
artefacts_by_input[i] = [sorted_info[idx_multi-1][0]]
LOGGER.info(
f'Keeping only the {idx_multi}th scan found for '
f'{i}: {sorted_info[idx_multi-1][0]}'
)

elif iv['artefact_type'] == 'assessor':
for cassr in assrs:
proctype = cassr.get('PROCTYPE')
Expand Down
69 changes: 51 additions & 18 deletions dax/rcq/analysislauncher.py
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Original file line number Diff line number Diff line change
Expand Up @@ -359,22 +359,52 @@ def get_session_inputs(self, spec, info, subject, session):
for scan_spec in spec.get('scans', []):
logger.debug(f'scan_spec={scan_spec}')

# Get list of resources to download from this scan
resources = scan_spec.get('resources', [])

# Check for nifti tag
if 'nifti' in scan_spec:
# Add a NIFTI resource using value as fdest
resources.append({
'resource': 'NIFTI',
'fdest': scan_spec['nifti']
})

scan_types = scan_spec['types'].split(',')

logger.debug(f'scan_types={scan_types}')

for scan in [x for x in scans if x['SCANTYPE'] in scan_types]:
input_scans = [x for x in scans if x['SCANTYPE'] in scan_types]

# Get list of resources to download from this scan
resources = scan_spec.get('resources', [])
if len(input_scans) > 0 and scan_spec.get('keep_multis', '') != 'all':
# Sort by id
input_scans = sorted(input_scans, lambda: x: x['SCANID'])
num_scans = len(input_scans)

# Check for nifti tag
if 'nifti' in scan_spec:
# Add a NIFTI resource using value as fdest
resources.append({
'resource': 'NIFTI',
'fdest': scan_spec['nifti']
})
# Apply keep_multis filter
if scan_spec['keep_multis'] == 'first':
idx_multi = 1
elif iv['keep_multis'] == 'last':
idx_multi = num_scans
else:
try:
idx_multi = int(iv['keep_multis'])
except:
msg = 'keep_multis must be first, last, or index 1,2,3,...'
logger.error(msg)
raise Exception(msg)

if idx_multi > num_scans:
msg = f'{idx_multi} index exceeds found {num_scans}'
logger.error(msg)
raise Exception(msg)

# Get a list of only the requested scan
input_scans = [input_scans[idx_multi-1]]

# Get the file inputs for each input scan
for scan in input_scans:
scanid = scan['SCANID']

for res_spec in resources:
try:
Expand All @@ -384,7 +414,7 @@ def get_session_inputs(self, spec, info, subject, session):
continue

# Get the download destination subdir
ddest = f'{subject}/{session}'
ddest = f'{subject}/{session}/scans/{scanid}'
if res_spec.get('ddest', False):
ddest += '/' + res_spec.get('ddest')

Expand All @@ -396,7 +426,7 @@ def get_session_inputs(self, spec, info, subject, session):
scan['SCANID'],
res
)
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{session}/scans/{scan["SCANID"]}/resources/{res}/files/{_file}'
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{session}/scans/{scanid}/resources/{res}/files/{_file}'
inputs.append(self._input(
fpath,
'FILE',
Expand Down Expand Up @@ -438,11 +468,12 @@ def get_session_inputs(self, spec, info, subject, session):
logger.debug(f'assr_types={assr_types}')

for assr in [x for x in assessors if x['PROCTYPE'] in assr_types]:
assrlabel = assr["ASSR"]

for res_spec in assr_spec['resources']:

# Get the download destination subdir
ddest = f'{subject}/{session}'
ddest = f'{subject}/{session}/assessors/{assrlabel}'
if res_spec.get('ddest', False):
ddest += '/' + res_spec.get('ddest')

Expand All @@ -454,15 +485,15 @@ def get_session_inputs(self, spec, info, subject, session):

if 'fmatch' in res_spec:
for fmatch in res_spec['fmatch'].split(','):
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{session}/assessors/{assr["ASSR"]}/out/resources/{res}/files/{fmatch}'
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{session}/assessors/{assrlabel}/out/resources/{res}/files/{fmatch}'
inputs.append(self._input(
fpath,
'FILE',
res_spec.get('fdest', fmatch),
ddest))
else:
# whole resource
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{session}/assessors/{assr["ASSR"]}/out/resources/{res}/files'
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{session}/assessors/{assrlabel}/out/resources/{res}/files'
inputs.append(self._input(
fpath,
'DIR',
Expand All @@ -481,6 +512,8 @@ def get_subject_inputs(self, spec, info, subject):
sgp = [x for x in info['sgp'] if x['SUBJECT'] == subject]

for assr in sgp:
assrlabel = assr['ASSR']

for assr_spec in sgp_spec:
logger.debug(f'assr_spec={assr_spec}')
assr_types = assr_spec['types'].split(',')
Expand All @@ -494,7 +527,7 @@ def get_subject_inputs(self, spec, info, subject):
for res_spec in assr_spec['resources']:

# Get the download destination subdir
ddest = f'{subject}'
ddest = f'{subject}/assessors/{assrlabel}'
if res_spec.get('ddest', False):
ddest += '/' + res_spec.get('ddest')

Expand All @@ -508,7 +541,7 @@ def get_subject_inputs(self, spec, info, subject):
if 'fmatch' in res_spec:
# Add each file
for fmatch in res_spec['fmatch'].split(','):
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{assr["ASSR"]}/resources/{res}/files/{fmatch}'
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{assrlabel}/resources/{res}/files/{fmatch}'
inputs.append(self._input(
fpath,
'FILE',
Expand All @@ -517,7 +550,7 @@ def get_subject_inputs(self, spec, info, subject):
))
else:
# We want the whole resource as one download
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{assr["ASSR"]}/resources/{res}/files'
fpath = f'data/projects/{info["name"]}/subjects/{subject}/experiments/{assrlabel}/resources/{res}/files'
inputs.append(self._input(
fpath,
'DIR',
Expand Down