Skip to content

fid_proc support and various bug fixes #32

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
VKarlaftis wants to merge 4 commits into
base: master
Choose a base branch
from
Open

fid_proc support and various bug fixes #32

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
30aba93
[skip ci] adding 'fid_proc" format and various bug fixes
VKarlaftis Jan 28, 2026
e256e8f
Merge branch 'master' of https://github.com/VKarlaftis/brukerapi-python
VKarlaftis Feb 3, 2026
6d4399a
[skip ci] relaxed file size check code
VKarlaftis Feb 3, 2026
3ab6e13
bug fix on subject file for fid_proc
VKarlaftis Feb 12, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion brukerapi/config/properties_fid_custom.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@
"dwell_s": [
{
"cmd": "1./ @sw_hz / 2.",
"conditions": []
"conditions": ["@sw_hz!=0"]
}
],
"TR": [
Expand Down
41 changes: 30 additions & 11 deletions brukerapi/dataset.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,10 +40,16 @@
"load": LOAD_STAGES["all"],
"mmap": False,
},
"2dseq": {
"parameter_files": ["visu_pars"],
"property_files": [Path(__file__).parents[0] / "config/properties_2dseq_core.json", Path(__file__).parents[0] / "config/properties_2dseq_custom.json"],
"load": LOAD_STAGES["all"],
'fid_proc': {
"parameter_files" : ['acqp', 'method'],
"property_files": [Path(__file__).parents[0] / 'config/properties_fid_core.json', Path(__file__).parents[0] / 'config/properties_fid_custom.json'],
"load": LOAD_STAGES['all'],
"mmap": False
},
'2dseq': {
"parameter_files": ['visu_pars'],
"property_files": [Path(__file__).parents[0] / 'config/properties_2dseq_core.json', Path(__file__).parents[0] / 'config/properties_2dseq_custom.json'],
"load": LOAD_STAGES['all'],
"scale": True,
"mmap": False,
},
Expand Down Expand Up @@ -77,6 +83,15 @@
"AdjStatePerScan": "./AdjStatePerScan",
"AdjStatePerStudy": "../AdjStatePerStudy",
},
"fid_proc": {
"method": "../../method",
"acqp": "../../acqp",
"subject": "../../../subject",
"reco": "./reco",
"visu_pars": "./visu_pars",
"AdjStatePerScan": "../../AdjStatePerScan",
"AdjStatePerStudy": "../../../AdjStatePerStudy",
},
"2dseq": {
"method": "../../method",
"acqp": "../../acqp",
Expand Down Expand Up @@ -156,7 +171,7 @@ def __init__(self, path, **state):
containing it. It is possible, to create an empty object using the load switch.

:param path: **str** path to dataset
:raise: :UnsuportedDatasetType: In case `Dataset.type` is not in SUPPORTED
:raise: :UnsupportedDatasetType: In case `Dataset.type` is not in SUPPORTED
:raise: :IncompleteDataset: If any of the JCAMP-DX files, necessary to create a Dataset instance is missing

"""
Expand Down Expand Up @@ -248,8 +263,12 @@ def _validate(self):
raise UnsuportedDatasetType(self.type)

# Check whether all necessary JCAMP-DX files are present
if self._state.get("load") >= LOAD_STAGES["parameters"] and not (set(DEFAULT_STATES[self.type]["parameter_files"]) <= set(os.listdir(str(self.path.parent)))):
raise IncompleteDataset
if self._state.get('load') >= LOAD_STAGES['parameters']:
for i in DEFAULT_STATES[self.type]['parameter_files']:
param_path = self.path.parent / RELATIVE_PATHS[self.type][i]
if i not in set(os.listdir(str(param_path.parent))):
raise IncompleteDataset


def load(self):
"""
Expand Down Expand Up @@ -381,7 +400,8 @@ def load_properties(self):

def unload_properties(self):
for property in self._properties:
delattr(self, property)
if hasattr(self, property):
delattr(self,property)
self._properties = []
self._state["load_properties"] = False

Expand Down Expand Up @@ -486,7 +506,7 @@ def load_schema(self):
"""
Load the schema for given data set.
"""
if self.type == "fid":
if self.type in ["fid", "fid_proc"]:
self._schema = SchemaFid(self)
elif self.type == "2dseq":
self._schema = Schema2dseq(self)
Expand Down Expand Up @@ -547,10 +567,9 @@ def _read_binary_file(self, path, dtype, shape):
"""
# TODO debug with this
try:
assert os.stat(str(path)).st_size == np.prod(shape) * dtype.itemsize
assert os.stat(str(path)).st_size >= np.prod(shape) * dtype.itemsize
except AssertionError:
raise ValueError("Dimension mismatch") from AssertionError

return np.array(np.memmap(path, dtype=dtype, shape=shape, order="F")[:])

def _write_data(self, path):
Expand Down
1 change: 1 addition & 0 deletions brukerapi/schemas.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
# properties required for loading of the data array for each dataset type
REQUIRED_PROPERTIES = {
"fid": ["numpy_dtype", "channels", "block_size", "acq_lenght", "scheme_id", "block_count", "encoding_space", "permute", "k_space", "encoded_dim", "shape_storage", "dim_type"],
"fid_proc": ["numpy_dtype", "channels", "block_size", "acq_lenght", "scheme_id", "block_count", "encoding_space", "permute", "k_space", "encoded_dim", "shape_storage", "dim_type"],
"2dseq": [
"pv_version",
"numpy_dtype",
Expand Down