Add MR images and pixel_representation flag #1
Conversation
|
@rickardholmberg @rickardraysearch Should be fine to merge now! |
Fix PEP8 warnings in build_dicom.py
Output from dciodvfy.exe: Error - Missing attribute Type 2 Required Element=<RadiopharmaceuticalInformationSequence> Module=<PETIsotope> Error - Missing attribute Type 2 Required Element=<PatientOrientationCodeSequence> Module=<NMPETPatientOrientation> Error - Missing attribute Type 2 Required Element=<PatientGantryRelationshipCodeSequence> Module=<NMPETPatientOrientation>
README.md
Outdated
| @@ -3,7 +3,7 @@ dicomutils | |||
|
|
|||
| A set of utilities for working with DICOM files. | |||
|
|
|||
| The main utility is currently build_dicom, which can generate simple synthetic CT data, | |||
| The main utility is currently build_dicom, which can generate simple synthetic CT data, MR data, | |||
build_dicom.py
Outdated
| choices=['signed', 'unsigned'], | ||
| help='signed: Stored pixel value type is int16, unsigned: Stored pixel value type is uint16.') | ||
| parser.add_argument('--rescale-slope', dest='rescale_slope', type=float, | ||
| help="""Set the rescale slope (defaults - CT: 1.0, MR: 1.0).""") |
There was a problem hiding this comment.
Also, removed slope/icept for MR so removed from here too.
build_dicom.py
Outdated
| num_voxels=num_voxels, | ||
| voxel_size=voxel_size, | ||
| pixel_representation=pixel_representation, | ||
| rescale_slope=rescale_slope, |
There was a problem hiding this comment.
rescale_slope seems undefined?
build_dicom.py
Outdated
| @@ -138,6 +219,8 @@ def __call__(self, parser, namespace, values, option_string=None): | |||
| sb.current_study['PatientsBirthDate'] = series.patients_birthdate | |||
| if series.modality == "CT": | |||
| ib.build() | |||
| elif series.modality == "MR": | |||
| ib.build() | |||
| elif series.modality == "RTDOSE": | |||
| self.seriesbuilders['CT'].append(b) | ||
| return b | ||
|
|
||
| def build_mr(self, num_voxels, voxel_size, pixel_representation, center=None, column_direction=None, | ||
| row_direction=None, slice_direction=None): |
There was a problem hiding this comment.
rescale_slope & rescale_intercept?
There was a problem hiding this comment.
slope/icept not applicable for MR, it was a mistake to add it and it was later removed.
builders.py
Outdated
|
|
||
| def build_pt(self, num_voxels, voxel_size, pixel_representation, center=None, column_direction=None, | ||
| row_direction=None, slice_direction=None): | ||
| b = PTBuilder(self.current_study, num_voxels, voxel_size, pixel_representation, |
| voxel_size, | ||
| pixel_representation, | ||
| center=None, | ||
| column_direction=None, |
There was a problem hiding this comment.
rescale_slope & rescale_intercept?
There was a problem hiding this comment.
Not applicable for MR
| num_voxels, | ||
| voxel_size, | ||
| pixel_representation, | ||
| center=None, |
|
I think going forward it is risky to use default arguments in "backend" code, better to handle that kind of stuff in build_dicom.py. Otherwise there is a risk that the values are not passed down correctly without generating errors... |
|
ping @rickardraysearch |
|
Unexpectedly, I was allowed to push to this branch. Sorry for that - the last commit 3d8488c was only intended to be pull request comments... Other than that, it looks good! |
|
Ok, feel free to merge (I don't have write access). |
@rickardraysearch
Verified created images with dciodvfy.exe.