Open
Conversation
6 tasks
Comment on lines
+34
to
+38
| "source": [ | ||
| "file_name = '/mnt/share/ALC_ptychography_alignment/simulations/cylinder_tilt_30.nxs'\n", | ||
| "data = NEXUSDataReader(file_name=file_name).read()\n", | ||
| "show2D(data, slice_list=('angle',0))" | ||
| ] |
Member
There was a problem hiding this comment.
please can you add some text to say that the data is available on the share available internally to the tomography team
Member
|
Helpful demo for having a go with the volume shrinker :) |
Neonbluestoplight
left a comment
Neonbluestoplight
left a comment
There was a problem hiding this comment.
Hi @hrobarts,
Just a tiny error I'm facing with the supported backends but the tool itself is really well thought out!
| "vs = VolumeShrinker(data, recon_backend='astra')\n", | ||
| "ig_reduced = vs.run(limits={'horizontal_x':(10, 150), 'vertical':(5, 50)}, preview=True)" | ||
| ] | ||
| }, |
There was a problem hiding this comment.
Hi @hrobarts,
I am encountering an error when change recon_backend from 'astra' to 'tigre':
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[23], [line 2](notebook-cell:?execution_count=23&line=2)
1 vs = VolumeShrinker(data, recon_backend='tigre')
----> [2](notebook-cell:?execution_count=23&line=2) ig_reduced = vs.run(limits={'horizontal_x':(10, 150), 'vertical':(5, 50)}, preview=True)
File ~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/utilities/shrink_volume.py:168, in VolumeShrinker.run(self, limits, preview, method, **kwargs)
166 if method.lower() == 'manual':
167 mask_radius = kwargs.pop('mask_radius', None)
--> [168](/home/username/desktop/cil-demos/misc/~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/utilities/shrink_volume.py:168) recon, binning = self._get_recon(mask_radius=mask_radius)
170 self._plot_with_bounds(recon, bounds, binning)
172 return self.update_ig(self.data.geometry.get_ImageGeometry(), bounds)
File ~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/utilities/shrink_volume.py:203, in VolumeShrinker._get_recon(self, mask_radius)
200 ag = data_binned.geometry
201 ig = ag.get_ImageGeometry()
--> [203](/home/username/desktop/cil-demos/misc/~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/utilities/shrink_volume.py:203) fbp = self.recon_method(ig, ag)
204 recon = fbp(data_binned)
206 if mask_radius is not None:
File ~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/plugins/tigre/FBP.py:67, in FBP.__init__(self, image_geometry, acquisition_geometry, **kwargs)
63 if device != 'gpu':
64 raise ValueError("TIGRE FBP is GPU only. Got device = {}".format(device))
---> [67](/home/username/desktop/cil-demos/misc/~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/plugins/tigre/FBP.py:67) AcquisitionDimension.check_order_for_engine('tigre', acquisition_geometry)
68 ImageDimension.check_order_for_engine('tigre', image_geometry)
...
127 f"Expected dimension_label order {order_requested},"
128 f" got {tuple(geometry.dimension_labels)}."
129 f" Try using `data.reorder('{engine}')` to permute for {engine}")
ValueError: Expected dimension_label order (<AcquisitionDimension.ANGLE: 'angle'>, <AcquisitionDimension.VERTICAL: 'vertical'>, <AcquisitionDimension.HORIZONTAL: 'horizontal'>), got (<AcquisitionDimension.VERTICAL: 'vertical'>, <AcquisitionDimension.ANGLE: 'angle'>, <AcquisitionDimension.HORIZONTAL: 'horizontal'>). Try using `data.reorder('tigre')` to permute for tigreIt seems to be tied to the preview=True option specifically which would explain why it didn't show up in tests since there are no test cases for preview=True.
There was a problem hiding this comment.
This error can be passed by just using
data.reorder('tigre')
vs = VolumeShrinker(data, recon_backend='tigre')
ig_reduced = vs.run(limits={'horizontal_x':(10, 150), 'vertical':(5, 50)}, preview=True)But then another error is observed:
---------------------------------------------------------------------------
NotImplementedError Traceback (most recent call last)
Cell In[29], [line 4](notebook-cell:?execution_count=29&line=4)
1 data.reorder('tigre')
3 vs = VolumeShrinker(data, recon_backend='tigre')
----> [4](notebook-cell:?execution_count=29&line=4) ig_reduced = vs.run(limits={'horizontal_x':(10, 150), 'vertical':(5, 50)}, preview=True)
File ~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/utilities/shrink_volume.py:168, in VolumeShrinker.run(self, limits, preview, method, **kwargs)
166 if method.lower() == 'manual':
167 mask_radius = kwargs.pop('mask_radius', None)
--> [168](/home/username/desktop/cil-demos/misc/~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/utilities/shrink_volume.py:168) recon, binning = self._get_recon(mask_radius=mask_radius)
170 self._plot_with_bounds(recon, bounds, binning)
172 return self.update_ig(self.data.geometry.get_ImageGeometry(), bounds)
File ~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/utilities/shrink_volume.py:203, in VolumeShrinker._get_recon(self, mask_radius)
200 ag = data_binned.geometry
201 ig = ag.get_ImageGeometry()
--> [203](/home/username/desktop/cil-demos/misc/~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/utilities/shrink_volume.py:203) fbp = self.recon_method(ig, ag)
204 recon = fbp(data_binned)
206 if mask_radius is not None:
File ~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/plugins/tigre/FBP.py:71, in FBP.__init__(self, image_geometry, acquisition_geometry, **kwargs)
67 AcquisitionDimension.check_order_for_engine('tigre', acquisition_geometry)
68 ImageDimension.check_order_for_engine('tigre', image_geometry)
---> [71](/home/username/desktop/cil-demos/misc/~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/plugins/tigre/FBP.py:71) tigre_geom, tigre_angles = CIL2TIGREGeometry.getTIGREGeometry(image_geometry,acquisition_geometry)
...
---> [96](/home/username/desktop/cil-demos/misc/~/miniforge3/envs/cil_dev/lib/python3.12/site-packages/cil/plugins/tigre/Geometry.py:96) raise NotImplementedError ("CIL cannot use TIGRE to process parallel geometries with tilted axes")
98 self.DSO = clearance_len
99 self.DSD = 2*clearance_len
NotImplementedError: CIL cannot use TIGRE to process parallel geometries with tilted axesWhich confuses me a bit because the code runs completely fine with Preview=False
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Example notebook demonstrating functionality of the VolumeShrinker tool