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adapt mia_processes to new version of populse_mia (populse_db V3) #89

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adapt mia_processes to new version of populse_mia (populse_db V3) #89

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4414ac3
adapt mia_processes to populse_db V3, 1
servoz Jan 23, 2025
b4eaf9f
adapt mia_processes to populse_db V3, 2
servoz Feb 4, 2025
d1c05c0
Merge branch 'master' into db_v3
servoz Feb 4, 2025
ca2e5fe
Merge branch 'master' into db_v3
servoz Feb 7, 2025
1f23733
Merge branch 'master' into db_v3
servoz Feb 17, 2025
6fbeec6
Merge branch 'master' into db_v3
servoz Mar 5, 2025
6b52384
Merge branch 'master' into db_v3
servoz Apr 1, 2025
c1ecac2
Merge branch 'master' into db_v3
servoz Apr 9, 2025
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31 changes: 20 additions & 11 deletions mia_processes/bricks/preprocess/spm/spatial_preprocessing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,14 @@
from nipype.interfaces.spm.base import ImageFileSPM

# populse_mia imports
from populse_mia.data_manager.project import COLLECTION_CURRENT
# from populse_mia.data_manager.project import COLLECTION_CURRENT
from populse_mia.data_manager import (
COLLECTION_CURRENT,
FIELD_TYPE_LIST_FLOAT,
FIELD_TYPE_STRING,
TAG_ORIGIN_USER,
TAG_UNIT_MM,
)
from populse_mia.software_properties import Config
from populse_mia.user_interface.pipeline_manager.process_mia import ProcessMIA

Expand Down Expand Up @@ -682,8 +689,10 @@ def _namesFilter(self):
files = []

if self.runFlag is False:

for file_name in self.apply_to_files:
if type(file_name) in [list, TraitListObject]:

if isinstance(file_name, (list, TraitListObject)):
file_name = file_name[0]

if self.in_filter == "GM" and os.path.basename(
Expand Down Expand Up @@ -1883,28 +1892,28 @@ def list_outputs(self, is_plugged=None, iteration=False):
# in database
tag_to_add = dict()
tag_to_add["name"] = "Voxel sizes"
tag_to_add["field_type"] = "list_float"
tag_to_add["field_type"] = FIELD_TYPE_LIST_FLOAT
tag_to_add["description"] = (
"The voxel sizes (x, y & "
"z, in mm) of the written "
"normalised images"
)
tag_to_add["visibility"] = True
tag_to_add["origin"] = "user"
tag_to_add["unit"] = "mm"
tag_to_add["origin"] = TAG_ORIGIN_USER
tag_to_add["unit"] = TAG_UNIT_MM
tag_to_add["default_value"] = None
tag_to_add["value"] = self.write_voxel_sizes
all_tags_to_add.append(tag_to_add)
# Add the Affine regularization type for
# normalization, in database
tag_to_add = dict()
tag_to_add["name"] = "Affine regularization type"
tag_to_add["field_type"] = "string"
tag_to_add["field_type"] = FIELD_TYPE_STRING
tag_to_add["description"] = (
"Standard space for affine " "registration"
"Standard space for affine registration"
)
tag_to_add["visibility"] = True
tag_to_add["origin"] = "user"
tag_to_add["origin"] = TAG_ORIGIN_USER
tag_to_add["unit"] = None
tag_to_add["default_value"] = None
tag_to_add["value"] = (
Expand Down Expand Up @@ -3205,14 +3214,14 @@ def list_outputs(self, is_plugged=None, iteration=False):
# Add the fwhm parameter for smooth, in database
tag_to_add = dict()
tag_to_add["name"] = "FWHM (X, Y, Z) for Smooth"
tag_to_add["field_type"] = "list_float"
tag_to_add["field_type"] = FIELD_TYPE_LIST_FLOAT
tag_to_add["description"] = (
"Full width at half maximum (FWHM) of the "
"Gaussian smoothing kernel in mm"
)
tag_to_add["visibility"] = True
tag_to_add["origin"] = "user"
tag_to_add["unit"] = "mm"
tag_to_add["origin"] = TAG_ORIGIN_USER
tag_to_add["unit"] = TAG_UNIT_MM
tag_to_add["default_value"] = None
tag_to_add["value"] = self.fwhm
all_tags_to_add.append(tag_to_add)
Expand Down
3 changes: 1 addition & 2 deletions mia_processes/bricks/stat/spm/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,7 @@
traits,
)
from nipype.interfaces.spm.base import ImageFileSPM
from populse_db.database import FIELD_TYPE_INTEGER
from populse_mia.data_manager.database_mia import TAG_ORIGIN_USER
from populse_mia.data_manager import FIELD_TYPE_INTEGER, TAG_ORIGIN_USER

# populse_db and populse_mia import
from populse_mia.data_manager.project import COLLECTION_CURRENT
Expand Down