Save gradient data as image #216
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…to analysis/variable_count_and_size_experiment
…lpack into analysis/variable_count_and_size_experiment
* return count as integer * allow specifying seed list in the recipe
…lpack into fix/parallel_packing_with_simularium
* add sphere mesh objects for tests * add recipe for nested mesh testing
…riable_count_and_size_experiment
* move voxelization code to environment * add voxelization function for gradient distances and weights * refactor image writer export code * add recipe and config for testing
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## main #216 +/- ##
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Coverage 98.63% 98.63%
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Packing analysis reportAnalysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST
Packing imageDistance analysisExpected minimum distance: 50.00
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Use |
| "voxel_size": [1,1,1], | ||
| "projection_axis": "z" | ||
| }, | ||
| "save_gradient_data_as_image": true |
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since this is a new config setting it should also have a default setting in the config loader.
I also think, for clarity, any settings here that are defaults should be removed. The configs are ballooning a bit
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Removed the default entries from the config file and added the new setting to config_loader.py
| @@ -70,6 +70,9 @@ def pack(recipe, config_path=None, analysis_config_path=None): | |||
| recipe_version=recipe_data["version"], | |||
| image_export_options=packing_config_data.get("image_export_options"), | |||
| parallel=packing_config_data.get("parallel", False), | |||
| save_gradient_data_as_image=packing_config_data.get( | |||
| "save_gradient_data_as_image", False | |||
| ), | |||
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this is starting to make me think we should just send the config into analysis instead of unpacking values here
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Created an issue #227 to track this
| @@ -3129,50 +3129,47 @@ def applyStep(self, step): | |||
| self.traj.applyState_primitive_name(self, step) | |||
| # ho can we apply to parent instance the rotatiotn? | |||
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| def create_voxelization(self, image_data, image_size, voxel_size, hollow=False): | |||
| def create_voxelization(self, image_writer): | |||
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Good idea to trim down the parameters and make this function more flexible!
Note: Merge #215 before this PR
Problem
We want to export grid distances and weights as 3D images.
Closes #199
Solution
Used the
ImageWriterclass to export gradient distances and weights as 3D tiff images.Type of change
Change summary:
Steps to Verify:
pack -r cellpack/tests/recipes/v2/test_nested_mesh_gradient.json -c cellpack/tests/packing-configs/test_gradient_data_image.jsonfigures/gradient_data_figuresto view the exported image.Screenshots:
Distances (mean intensity projection):
Weights (mean intensity projection):
Keyfiles (delete if not relevant):
ImageWriter.pyGradients.py