formatting

src/depiction/tools/simulate/synthetic_msi_data_generator.py

@@ -12,6 +12,7 @@
 
 # TODO configure shifts
 
+
 class SyntheticMSIDataGenerator:
     """Helper that creates synthetic MSI data."""
 

src/depiction_targeted_preproc/pipeline_config/model.py

@@ -93,8 +93,8 @@ class SimulateParameters(Model):
     image_height: int = 100
     n_labels: int = 30
     bin_width_ppm: float = 100.0
-    target_mass_min: float = 850.
-    target_mass_max: float = 1900.
+    target_mass_min: float = 850.0
+    target_mass_max: float = 1900.0
 
 
 class PipelineArtifact(str, Enum):

src/depiction_targeted_preproc/workflow/qc/plot_calibration_map.py

@@ -41,7 +41,9 @@ def qc_plot_calibration_map(
 
     vis_shifts = VisualizeMassShiftMap(models=models, coordinates=coords_2d)
     # TODO fix same_scale
-    fig, axs = vis_shifts.plot_test_mass_maps_and_histograms(test_masses=test_masses, same_scale=True, int_limits=(-.25, .25))
+    fig, axs = vis_shifts.plot_test_mass_maps_and_histograms(
+        test_masses=test_masses, same_scale=True, int_limits=(-0.25, 0.25)
+    )
     fig.savefig(output_pdf)
     fig.clear()
 

src/depiction_targeted_preproc/workflow/qc/plot_calibration_map_v2.py

@@ -16,14 +16,14 @@ def qc_plot_calibration_map_v2(
     fig, axs = plt.subplots(2, 1, figsize=(10, 20))
 
     # show the map
-    mass_shifts.isel(c=0).plot.imshow(x="x", y="y", ax=axs[0], cmap="coolwarm", vmin=-0.5, vmax=+.5)
+    mass_shifts.isel(c=0).plot.imshow(x="x", y="y", ax=axs[0], cmap="coolwarm", vmin=-0.5, vmax=+0.5)
     axs[0].set_aspect("equal")
     test_mass = mass_shifts.coords["c"][0]
     axs[0].set_title(f"Computed shift for test mass {test_mass:.2f}")
 
     # show the histogram
     # TODO the clipping could be misleading (as it's not indicated)
-    mass_shifts.isel(c=0).clip(-.5, .5).plot.hist(ax=axs[1], bins=100, color="gray")
+    mass_shifts.isel(c=0).clip(-0.5, 0.5).plot.hist(ax=axs[1], bins=100, color="gray")
     axs[1].set_title("Histogram of computed shifts")
 
     plt.savefig(output_pdf, bbox_inches="tight")