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Optimizations of jcampdx readin, faster file transfer, Support for rawdata, fix EPSI and dtiEPI fids bump version #31

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Merged
headmeister merged 5 commits into from
Feb 2, 2026
Merged

Optimizations of jcampdx readin, faster file transfer, Support for rawdata, fix EPSI and dtiEPI fids bump version #31

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95bdf22
much faster fiolder creation and traversal
Jan 31, 2026
46bb925
jcampdx optimizations
Jan 31, 2026
30e2280
support for PV360 and PV7 rawdata
Feb 1, 2026
12b3ed3
fix loading EPSI and dtiEPI sizes
Feb 1, 2026
de4f0cd
bump version and readme
Feb 2, 2026
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52 changes: 3 additions & 49 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -164,54 +164,7 @@ Compatible pulse sequences for **fid** data sets:
* STEAM.ppg
* igFLASH.ppg

ParaVision v6.0.1
"""""""""""""""""
Compatible data set types:

* **fid**
* **2dseq**
* **rawdata.job0**
* **rawdata.Navigator**

Compatible pulse sequences for **fid** data sets:

* FLASH.ppg,
* FLASHAngio.ppg
* IgFLASH.ppg
* MGE.ppg
* MSME.ppg
* RARE.ppg
* FAIR_RARE.ppg
* RAREVTR.ppg
* RAREst.ppg
* MDEFT.ppg
* FISP.ppg
* FLOWMAP.ppg
* DtiStandard.ppg
* EPI.ppg
* FAIR_EPI.ppg
* CASL_EPI.ppg
* DtiEpi.ppg
* T1_EPI.ppg
* T2_EPI.ppg
* T2S_EPI.ppg
* SPIRAL.ppg
* DtiSpiral.ppg
* UTE.ppg
* UTE3D.ppg
* ZTE.ppg
* CSI.ppg
* FieldMap.ppg
* SINGLEPULSE.ppg
* NSPECT.ppg
* EPSI.ppg
* PRESS.ppg
* STEAM.ppg
* ISIS.ppg
* CPMG.ppg
* RfProfile.ppg

ParaVision v7.0.0
ParaVision v6.0.1 and v7.0.0
"""""""""""""""""
Compatible data set types:

Expand Down Expand Up @@ -259,8 +212,9 @@ Compatible pulse sequences for **fid** data sets:
* RfProfile.ppg


ParaVision v360
ParaVision 360 v1.1 v3.0-v3.7
"""""""""""""""
Reading rawdata is supported only in a basic form, no reshaping into k-space is supported at the moment.
Compatible data set types:

* **2dseq**
Expand Down
69 changes: 63 additions & 6 deletions brukerapi/config/properties_fid_core.json
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Original file line number Diff line number Diff line change
Expand Up @@ -223,9 +223,7 @@
["#PULPROG[1:-1]",
[
"EPI.ppg",
"DtiEpi.ppg",
"navigatorEPI_OM.ppg",
"EPSI.ppg",
"FAIR_EPI.ppg",
"CASL_EPI.ppg",
"T1_EPI.ppg",
Expand All @@ -236,6 +234,18 @@
"#ACQ_sw_version in ['<PV 5.1>', '<PV 6.0>', '<PV 6.0.1>', '<PV-7.0.0>']"
]
},
{
"cmd": "'dEPI'" ,
"conditions": [
["#PULPROG[1:-1]",
[
"DtiEpi.ppg",
"EPSI.ppg"
]
],
"#ACQ_sw_version in ['<PV 5.1>', '<PV 6.0>', '<PV 6.0.1>', '<PV-7.0.0>']"
]
},
{
"cmd": "'SPECTROSCOPY'" ,
"conditions": [
Expand Down Expand Up @@ -322,7 +332,13 @@
]
},
{
"cmd": "#NR",
"cmd": "#NSegments*#NI*#NR*(#ACQ_size[2] if len(#ACQ_size)>2 else 1)",
"conditions": [
"@scheme_id=='dEPI'"
]
},
{
"cmd": "#NR*#NI",
"conditions": [
"@scheme_id=='SPECTROSCOPY'"
]
Expand Down Expand Up @@ -430,9 +446,23 @@
"@scheme_id=='EPI'"
]
},
{
"cmd": [
"#PVM_EncMatrix[0] * #PVM_EncMatrix[1] // #NSegments",
"#PVM_EncNReceivers",
"#NSegments",
"#NI",
"#NR",
"#ACQ_size[2] if len(#ACQ_size)>2 else 1"
],
"conditions": [
"@scheme_id=='dEPI'"
]
},
{
"cmd": [
"#ACQ_size.tuple[0] // 2",
"#NI",
"#NR"
],
"conditions": [
Expand Down Expand Up @@ -527,11 +557,24 @@
{
"cmd": [0,2,3,4,1],
"conditions": [
"@scheme_id in ['EPI', 'SPIRAL']"
"@scheme_id in ['SPIRAL']"
]
},
{
"cmd": [0,2,3,4,1],
"conditions": [
"@scheme_id in ['EPI']"
]
},
{
"cmd": [0,2,3,4,1,5],
"conditions": [
"@scheme_id in ['dEPI']"
]
},

{
"cmd": [0,1],
"cmd": [0,1,2],
"conditions": [
"@scheme_id=='SPECTROSCOPY'"
]
Expand Down Expand Up @@ -604,9 +647,23 @@
"@scheme_id=='EPI'"
]
},
{
"cmd": [
"#PVM_EncMatrix[0]",
"#PVM_EncMatrix[1]",
"#NI",
"#NR",
"#PVM_EncNReceivers",
"#ACQ_size[2] if len(#ACQ_size)>2 else 1"
],
"conditions": [
"@scheme_id=='dEPI'"
]
},
{
"cmd": [
"#ACQ_size.tuple[0] // 2",
"#NI",
"#NR"
],
"conditions": [
Expand Down Expand Up @@ -701,7 +758,7 @@
"'channel'"
],
"conditions": [
["@scheme_id",["CART_2D","RADIAL","EPI","SPIRAL","ZTE"]]
["@scheme_id",["CART_2D","RADIAL","EPI","dEPI","SPIRAL","ZTE"]]
]
},
{
Expand Down
25 changes: 16 additions & 9 deletions brukerapi/config/properties_rawdata_core.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,65 +5,72 @@
"conditions": [
"#GO_raw_data_format=='GO_32BIT_SGN_INT'",
"#BYTORDA=='little'",
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
]
},
{
"cmd": "np.dtype('int16').newbyteorder('<')",
"conditions": [
"#GO_raw_data_format=='GO_16BIT_SGN_INT'",
"#BYTORDA=='little'",
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
]
},
{
"cmd": "np.dtype('float32').newbyteorder('<')",
"conditions": [
"#GO_raw_data_format=='GO_32BIT_FLOAT'",
"#BYTORDA=='little'",
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
]
},
{
"cmd": "np.dtype('int32').newbyteorder('>')",
"conditions": [
"#GO_raw_data_format=='GO_32BIT_SGN_INT'",
"#BYTORDA=='big'",
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
]
},
{
"cmd": "np.dtype('int16').newbyteorder('>')",
"conditions": [
"#GO_raw_data_format=='GO_16BIT_SGN_INT'",
"#BYTORDA=='big'",
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
]
},
{
"cmd": "np.dtype('float32').newbyteorder('>')",
"conditions": [
"#GO_raw_data_format=='GO_32BIT_FLOAT'",
"#BYTORDA=='big'",
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>"]]
["#ACQ_sw_version",["<PV 5.1>", "<PV 6.0>", "<PV 6.0.1>","<PV-7.0.0>"]]
]
},
{
"cmd": "np.dtype('i4').newbyteorder('<')",
"conditions": [
"#ACQ_word_size=='_32_BIT'",
"#BYTORDA=='little'",
["#ACQ_sw_version",["<PV-360.1.1>"]]
["#ACQ_sw_version",["<PV-360.1.1>","<PV-360.3.0>","<PV-360.3.1>","<PV-360.3.2>","<PV-360.3.3>","<PV-360.3.4>","<PV-360.3.5>","<PV-360.3.6>","<PV-360.3.7>"]]
]
}
],
"job_desc": [
{
"cmd": "#ACQ_jobs.primed_dict(7)['<{}>'.format(@subtype)]",
"conditions": [
"#ACQ_sw_version in ['<PV-360.1.1>']"
["#ACQ_sw_version",["<PV-360.1.1>"]]
]
},
{
"cmd": "[v for v in #ACQ_jobs.nested if v[-1] == '<{}>'.format(@subtype)][0]",
"conditions": [
["#ACQ_sw_version",["<PV-360.3.0>","<PV-360.3.1>","<PV-360.3.2>","<PV-360.3.3>","<PV-360.3.4>","<PV-360.3.5>","<PV-360.3.6>","<PV-360.3.7>"]]
]
},

{
"cmd": "#ACQ_jobs.nested[0]",
"conditions": [
Expand All @@ -88,7 +95,7 @@
],
"shape_storage": [
{
"cmd": "(@job_desc[0],) + (@job_desc[3],)",
"cmd": "(@job_desc[0],) + (#PVM_EncNReceivers,) + (@job_desc[3],)",
"conditions": []
}
]
Expand Down
66 changes: 65 additions & 1 deletion brukerapi/config/properties_rawdata_custom.json
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Original file line number Diff line number Diff line change
@@ -1 +1,65 @@
{}
{
"subj_id": [
{
"cmd": "#SUBJECT_id[1:-1]",
"conditions": [

]
},
{
"cmd": "''",
"conditions": [

]
}
],
"study_id": [
{
"cmd": "str(#SUBJECT_study_nr)",
"conditions": [

]
},
{
"cmd": "''",
"conditions": [

]
}
],
"exp_id": [
{
"cmd": "@path.parent.name",
"conditions": [

]
},
{
"cmd": "''",
"conditions": [

]
}
],
"id": [
{
"cmd": "f'RawData_{@subtype}_{@exp_id}_{@subj_id}_{@study_id}'",
"conditions": [
]
}
],
"TR": [
{
"cmd": "#PVM_RepetitionTime",
"conditions": [],
"unit": "ms"
}
],
"TE": [
{
"cmd": "#PVM_EchoTime",
"conditions": [],
"unit": "ms"
}
]
}
10 changes: 5 additions & 5 deletions brukerapi/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -546,10 +546,10 @@ def _read_binary_file(self, path, dtype, shape):
1D ndarray containing the full data vector
"""
# TODO debug with this
# try:
# assert os.stat(str(path)).st_size == np.prod(shape) * dtype.itemsize
# except AssertionError:
# raise ValueError('Dimension missmatch')
try:
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")[:])

Expand Down Expand Up @@ -594,7 +594,7 @@ def write(self, path, **kwargs):

path = Path(path)

if path.name != self.type:
if path.name.split(".")[0] != self.type:
raise DatasetTypeMissmatch

parent = path.parent
Expand Down
2 changes: 1 addition & 1 deletion brukerapi/folders.py
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Original file line number Diff line number Diff line change
Expand Up @@ -217,7 +217,7 @@ def make_tree(self, *, recursive: bool = True) -> list:
children.append(Folder(path, parent=self, recursive=recursive, dataset_index=self._dataset_index, dataset_state=self._dataset_state))
continue

if path.name in self._dataset_index:
if path.name in self._dataset_index or (path.name.partition(".")[0] in self._dataset_index and "rawdata" in path.name):
try:
children.append(Dataset(path, **self._dataset_state))
except (UnsuportedDatasetType, IncompleteDataset, NotADatasetDir):
Expand Down
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