Merge pull request #104 from Lucaslab-Berkeley/jd_movie_refine_template

Add ability to refine_template from a movie

Author: jdickerson95

programs/refine_template/refine_template_example_config.yaml

@@ -37,4 +37,11 @@ preprocessing_filters:
     low_freq_cutoff: null
 computational_config:
   gpu_ids: 0
-  num_cpus: 1
+  num_cpus: 1
+apply_global_filtering: true
+movie_config:
+  enabled: false
+  movie_path: path/to/aligned_movie.mrc
+  deformation_field_path: path/to/deformation_field.csv
+  pre_exposure: 0.0
+  fluence_per_frame: 1.0

pyproject.toml

@@ -48,12 +48,16 @@ dependencies = [
     "types-PyYAML",
     "roma",
     "tqdm",
-    "torch-fourier-slice>=v0.2.0",
+    "torch-fourier-slice>=v0.4.0",
     "torch-fourier-filter>=v0.2.6",
     "torch-so3>=v0.2.0",
     "ttsim3d>=v0.4.0",
     "lmfit",
     "zenodo-get",
+    "torch-fourier-shift",
+    "torch-motion-correction>=0.0.4",
+    "torch-grid-utils>=v0.0.9",
+    "torch-ctf"
 ]
 
 [tool.hatch.metadata]
@@ -153,7 +157,10 @@ pretty = true
 [tool.pytest.ini_options]
 minversion = "7.0"
 testpaths = ["tests"]
-filterwarnings = ["error"]
+filterwarnings = [
+    "error",
+    "ignore::FutureWarning",
+]
 addopts = "-m 'not slow'"               # Skip slow tests on default
 markers = ["slow: marks test as slow"]
 

src/leopard_em/analysis/__init__.py

@@ -6,7 +6,10 @@
     match_template_peaks_to_dict,
 )
 from .pvalue_metric import extract_peaks_and_statistics_p_value
-from .zscore_metric import extract_peaks_and_statistics_zscore, gaussian_noise_zscore_cutoff
+from .zscore_metric import (
+    extract_peaks_and_statistics_zscore,
+    gaussian_noise_zscore_cutoff,
+)
 
 __all__ = [
     "MatchTemplatePeaks",

src/leopard_em/backend/__init__.py

@@ -1,10 +1,12 @@
 """Submodule for computationally intensive backend functions."""
 
+from .core_differentiable_refine import core_differentiable_refine
 from .core_match_template import core_match_template
 from .core_refine_template import core_refine_template, cross_correlate_particle_stack
 
 __all__ = [
     "core_match_template",
     "core_refine_template",
     "cross_correlate_particle_stack",
+    "core_differentiable_refine",
 ]