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Label the acquisition-object axis for what it is, and keep slice distance a double (R2, R5, R6, D4) #163

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Merged
headmeister merged 8 commits into from
Jul 26, 2026
Merged

Label the acquisition-object axis for what it is, and keep slice distance a double (R2, R5, R6, D4) #163

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71da9f0
Derive the 2dseq affine from VisuCorePosition/VisuCoreOrientation
gdevenyi Jul 26, 2026
b313fbc
Join wrapped JCAMP-DX lines by deleting the break, and stop write() c…
gdevenyi Jul 26, 2026
c59ebd0
Parse escaped delimiters and nested structs instead of discarding them
gdevenyi Jul 26, 2026
0cf7170
Make FrameGroupSplitter.write() work and honour add_parameters=
gdevenyi Jul 26, 2026
7bb20c3
Read every acquired sample of an EPSI fid
gdevenyi Jul 26, 2026
d7a90d3
Read transposed frames in their stored shape and own frame-group meta…
gdevenyi Jul 26, 2026
10d7939
Reach PV360 raw data through Study, and read traj from an archive
gdevenyi Jul 26, 2026
675cfdc
Label the acquisition-object axis for what it is, and keep slice dist…
gdevenyi Jul 26, 2026
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113 changes: 4 additions & 109 deletions brukerapi/config/properties_2dseq_custom.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -111,35 +111,20 @@
"#VisuCoreDimDesc.list[2]=='spatial'"]
},
{
"cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreFrameThickness + #VisuCoreSlicePacksSliceDist.list[0]])",
"conditions": [
"#VisuCreatorVersion in ['<6.0.1>']",
"#VisuCoreDim==2"]
},
{
"cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], abs(#VisuCorePosition[0,2] - #VisuCorePosition[1,2])])",
"cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], np.linalg.norm(#VisuCorePosition[1,:] - #VisuCorePosition[0,:])])",
"conditions": [
"#VisuCreatorVersion in ['<5.1>']",
"#VisuCorePosition.size[0]>1",
"#VisuCoreDim==2"]
"#VisuCoreDim==2"],
"comment": "spec 7.10: the distance between two measured slice centres. VisuCoreSlicePacksSliceDist is already centre-to-centre, so it must not be added to VisuCoreFrameThickness"
},
{
"cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreFrameThickness])",
"cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreSlicePacksSliceDist.list[0]])",
"conditions": [
"#VisuCreatorVersion in ['<5.1>']",
"#VisuCorePosition.size[0]==1",
"#VisuCoreDim==2"]
},
{
"cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], np.linalg.norm(#VisuCorePosition[1,:] - #VisuCorePosition[0,:])])",
"conditions": [
"#VisuCorePosition.size[0]>1",
"#VisuCoreDim==2"]
},
{
"cmd": "np.array([#VisuCoreExtent[0] / #VisuCoreSize[0], #VisuCoreExtent[1] / #VisuCoreSize[1], #VisuCoreFrameThickness])",
"conditions": [
"#VisuCorePosition.size[0]==1",
"#VisuCoreDim==2"]
},
{
Expand All @@ -150,96 +135,6 @@
"#VisuCoreDimDesc.list[2]=='spatial'"]
}
],
"position_matrix": [
{
"cmd": "np.array([[np.cos(np.pi), -np.sin(np.pi), 0], [np.sin(np.pi), np.cos(np.pi), 0], [0, 0, 1]])",
"conditions": [
"#VisuSubjectPosition=='Head_Supine'"
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
},
{
"cmd": "np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])",
"conditions": [
"#VisuSubjectPosition=='Head_Prone'"
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
},
{
"cmd": "np.array([[np.cos(np.pi/2), -np.sin(np.pi/2), 0], [np.sin(np.pi/2), np.cos(np.pi/2), 0], [0, 0, 1]])",
"conditions": [
"#VisuSubjectPosition=='Head_Left'"
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
},
{
"cmd": "np.array([[np.cos(-np.pi/2), -np.sin(-np.pi/2), 0], [np.sin(-np.pi/2), np.cos(-np.pi/2), 0], [0, 0, 1]])",
"conditions": [
"#VisuSubjectPosition=='Head_Right'"
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
},
{
"cmd": "np.array([[1, 0, 0], [0, np.cos(np.pi), -np.sin(np.pi)], [0, np.sin(np.pi), np.cos(np.pi)]]).astype('float')",
"conditions": [
"#VisuSubjectPosition in ['Foot_Supine', 'Tail_Supine']"
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
},
{
"cmd": "np.array([[np.cos(np.pi), 0, np.sin(np.pi)], [0, 1, 0], [-np.sin(np.pi), 0, np.cos(np.pi)]]).astype('float')",
"conditions": [
"#VisuSubjectPosition in ['Foot_Prone', 'Tail_Prone']"
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
},
{
"cmd": "np.array([[np.cos(np.pi/2), -np.sin(np.pi/2), 0], [np.sin(np.pi/2), np.cos(np.pi/2), 0], [0, 0, 1]])",
"conditions": [
"#VisuSubjectPosition in ['Foot_Left', 'Tail_Left']"
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
},
{
"cmd": "np.array([[np.cos(-np.pi/2), -np.sin(-np.pi/2), 0], [np.sin(-np.pi/2), np.cos(-np.pi/2), 0], [0, 0, 1]])",
"conditions": [
"#VisuSubjectPosition in ['Foot_Right', 'Tail_Right']"
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
}
],
"rotation": [
{
"cmd": "np.dot(@position_matrix, np.reshape(#VisuCoreOrientation[0,:],(3,3)).T.dot(np.diag(@resolution)))",
"conditions": [
],
"reference": "This recipe was taken from the version BrkRaw repository (https://github.com/BrkRaw/bruker) version 0.3.4 (10.5281/zenodo.3907018)"
}
],
"position": [
{
"cmd": "#PVM_VoxArrPosition[0,:].astype(np.float64)",
"conditions": [
"#VisuCoreDimDesc.list[0]=='spectroscopic'",
"#VisuCoreDimDesc.list[1]=='spatial'",
"#VisuCoreDimDesc.list[2]=='spatial'"]
},
{
"cmd": "np.array([#VisuCorePosition[0,0] + @extent[0], #VisuCorePosition[0,1] + @extent[1], #VisuCorePosition[0,2]])",
"conditions": []
}
],
"affine": [
{
"cmd": "np.array([[@rotation[0,0], @rotation[0,1], @rotation[0,2], @position[0]],[@rotation[1,0], @rotation[1,1], @rotation[1,2], @position[1]],[@rotation[2,0], @rotation[2,1], @rotation[2,2], @position[2]],[0, 0, 0, 1]])",
"conditions": []
},
{
"cmd": "np.identity(4)",
"conditions": [],
"comment": "default value"
}
],
"TE": [
{
"cmd": "#VisuAcqEchoTime",
Expand Down
74 changes: 60 additions & 14 deletions brukerapi/config/properties_fid_core.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -134,19 +134,12 @@
"#GO_block_size=='Standard_KBlock_Format'"
]
},
{
"cmd": "int(2 * #PVM_DigNp * @channels // #NSegments)",
"conditions": [
"#GO_block_size!='Standard_KBlock_Format'",
"#PULPROG[1:-1]=='EPSI.ppg'"
]
},
{
"cmd": "int(2 * #PVM_DigNp * @channels)",
"conditions": [
"#GO_block_size!='Standard_KBlock_Format'",
"#PULPROG[1:-1]!='EPSI.ppg'"
]
"#GO_block_size!='Standard_KBlock_Format'"
],
"comment": "spec 3.1: for GO_block_size=continuous the whole block is digitized data. Dividing by NSegments here dropped every segment but the last, because block_count already counts segments"
},
{
"cmd": "#ACQ_jobs[0][0]",
Expand Down Expand Up @@ -343,6 +336,13 @@
"@scheme_id=='EPI'"
]
},
{
"cmd": "#NSegments*#ACQ_size[2]*#NI*#NR",
"conditions": [
"#GO_block_size!='Standard_KBlock_Format'",
"#PULPROG[1:-1]=='EPSI.ppg'"
]
},
{
"cmd": "#NSegments*#NI*#NR*(#ACQ_size[2] if len(#ACQ_size)>2 else 1)",
"conditions": [
Expand Down Expand Up @@ -475,6 +475,19 @@
"@scheme_id=='EPI'"
]
},
{
"cmd": [
"#PVM_EncMatrix[0]",
"#PVM_EncNReceivers",
"#PVM_DigNp // #PVM_EncMatrix[0]",
"#NSegments",
"#ACQ_size[2]"
],
"conditions": [
"#GO_block_size!='Standard_KBlock_Format'",
"#PULPROG[1:-1]=='EPSI.ppg'"
]
},
{
"cmd": [
"#PVM_EncMatrix[0] * #PVM_EncMatrix[1] // #NSegments",
Expand Down Expand Up @@ -604,6 +617,13 @@
"@scheme_id in ['EPI']"
]
},
{
"cmd": [0,4,3,2,1],
"conditions": [
"#GO_block_size!='Standard_KBlock_Format'",
"#PULPROG[1:-1]=='EPSI.ppg'"
]
},
{
"cmd": [0,2,3,4,1,5],
"conditions": [
Expand Down Expand Up @@ -701,6 +721,19 @@
"@scheme_id=='EPI'"
]
},
{
"cmd": [
"#PVM_EncMatrix[0]",
"#ACQ_size[2]",
"#NSegments * (#PVM_DigNp // #PVM_EncMatrix[0])",
"#PVM_EncNReceivers"
],
"conditions": [
"#GO_block_size!='Standard_KBlock_Format'",
"#PULPROG[1:-1]=='EPSI.ppg'"
],
"comment": "spec 6.3: matches RECO_inp_size -- read x phase x spectral points x receivers"
},
{
"cmd": [
"#PVM_EncMatrix[0]",
Expand Down Expand Up @@ -808,6 +841,7 @@
"'k_space_encode_step_0'",
"'k_space_encode_step_1'",
"'k_space_encode_step_2'",
"'object'",
"'repetition'",
"'channel'"
],
Expand All @@ -822,7 +856,19 @@
"cmd": [
"'k_space_encode_step_0'",
"'k_space_encode_step_1'",
"'slice'",
"'k_space_encode_step_2'",
"'channel'"
],
"conditions": [
"#GO_block_size!='Standard_KBlock_Format'",
"#PULPROG[1:-1]=='EPSI.ppg'"
]
},
{
"cmd": [
"'k_space_encode_step_0'",
"'k_space_encode_step_1'",
"'object'",
"'repetition'",
"'channel'",
"'k_space_encode_step_2'"
Expand All @@ -835,7 +881,7 @@
"cmd": [
"'k_space_encode_step_0'",
"'k_space_encode_step_1'",
"'slice'",
"'object'",
"'repetition'",
"'channel'"
],
Expand All @@ -858,8 +904,8 @@
{
"cmd": [
"'k_space_encode_step_0'",
"'repetition'",
"'average'"
"'object'",
"'repetition'"
],
"conditions": [
"@scheme_id=='SPECTROSCOPY'"
Expand Down
8 changes: 4 additions & 4 deletions brukerapi/config/properties_traj_core.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@
],
"shape_storage": [
{
"cmd": "(#ACQ_dim, int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #NPro), #NPro)",
"cmd": "(#ACQ_dim, int(file_size(self.path) // @numpy_dtype.itemsize // #ACQ_dim // #NPro), #NPro)",
"conditions": [
[
"@scheme_id",
Expand All @@ -88,7 +88,7 @@
]
},
{
"cmd": "(#ACQ_dim, int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #PVM_SpiralNbOfInterleaves), #PVM_SpiralNbOfInterleaves)",
"cmd": "(#ACQ_dim, int(file_size(self.path) // @numpy_dtype.itemsize // #ACQ_dim // #PVM_SpiralNbOfInterleaves), #PVM_SpiralNbOfInterleaves)",
"conditions": [
[
"@scheme_id",
Expand Down Expand Up @@ -122,7 +122,7 @@
{
"cmd": [
"#ACQ_dim",
"int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #NPro)",
"int(file_size(self.path) // @numpy_dtype.itemsize // #ACQ_dim // #NPro)",
"#NPro"
],
"conditions": [
Expand All @@ -138,7 +138,7 @@
{
"cmd": [
"#ACQ_dim",
"int(os.stat(self.path).st_size // @numpy_dtype.itemsize // #ACQ_dim // #PVM_SpiralNbOfInterleaves)",
"int(file_size(self.path) // @numpy_dtype.itemsize // #ACQ_dim // #PVM_SpiralNbOfInterleaves)",
"#PVM_SpiralNbOfInterleaves"
],
"conditions": [
Expand Down
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