cleaning

brick/component/extension.py

@@ -192,7 +192,6 @@ class extension_t(glial_cmp_t):
         result = image.copy()
         if (low is not None) and (high is not None):
             result = __HysterisisImage__(result, low, high)
-            # np_.save("D:\\MorganeNadal\\img512enhanced_norm_hyst_2.npy", result)
         if selem is not None:
             result = __MorphologicalCleaning__(result, selem)
 

nutrimorph.py

@@ -126,17 +126,15 @@ image = in_.ImageVerification(image, channel)
 # iv_.image_verification(image, channel)  # -> PySide2 user interface  # TODO: must return the modified image!
 # /!\ conflicts between some versions of PySide2 and Python3
 
-image = image[:, 512:, 512:]  # 512 # 562 # Just for development
+# image = image[:, 512:, 512:]  # 512 # 562 # Just for development
 img_shape = image.shape
 
-# np_.save("D:\\MorganeNadal\\img512.npy", image)
 #
 print(f"IMAGE: s.{img_shape} t.{image.dtype} m.{image.min()} M.{image.max()}")
 
 # Intensity relative normalization (between 0 and 1).
 image_for_soma = in_.IntensityNormalizedImage(image)
 image_for_ext = in_.IntensityNormalizedImage(image)
-# np_.save("D:\\MorganeNadal\\img512norm.npy", image_for_ext)
 
 print(f"NRM-IMG: t.{image_for_soma.dtype} m.{image_for_soma.min():.2f} M.{image_for_soma.max():.2f}")
 
@@ -213,13 +211,10 @@ enhanced_ext, ext_scales = extension_t.EnhancedForDetection(
     method,
     in_parallel=in_parallel)
 
-# np_.save("D:\\MorganeNadal\\img512enhanced.npy", enhanced_ext)
-
 elapsed_time = tm_.gmtime(tm_.time() - start_time)
 print(f"Elapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}\n")
 
 enhanced_ext = in_.IntensityNormalizedImage(enhanced_ext)
-# np_.save("D:\\MorganeNadal\\img512enhanced_norm.npy", enhanced_ext)
 
 # Creation of the enhanced maps
 ext_nfo["coarse_map"] = extension_t.CoarseMap(enhanced_ext, ext_low_c, ext_high_c, ext_selem_pixel_c) # seuillage
@@ -231,8 +226,6 @@ ext_nfo["lmp"], n_extensions = ms_.label(ext_nfo["map"], return_num=True)
 # ext_nfo["lmp"] = relabel_sequential(ext_lmp)[0]
 # n_extensions = ext_nfo["lmp"].max()
 
-# np_.save("D:\\MorganeNadal\\img512enhanced_norm_hyst_morpho_2.npy", ext_nfo["lmp"])
-
 extensions = tuple(
     extension_t().FromMap(ext_nfo["lmp"], ext_scales, uid)
     for uid in range(1, n_extensions + 1))
@@ -372,8 +365,6 @@ print(f"\nElapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}")
 if with_plot:
     pl_.show()
 
-# np_.save("D:\\MorganeNadal\\img512final_2.npy", som_nfo['soma_w_ext_lmp'])
-
 po_.MaximumIntensityProjectionZ(som_nfo['soma_w_ext_lmp'])
 
 # --- Extract all the extensions of all somas as a graph
@@ -423,7 +414,7 @@ bins_curvature[-1] = np_.inf
 
 # DF creation
 features_df = ge_.ExtractFeaturesInDF(somas, size_voxel_in_micron, bins_length, bins_curvature, ext_scales)
-features_df.to_csv("D:\\MorganeNadal\\M2 report\\features_512_.csv")
+features_df.to_csv("...\\features.csv")
 
 #
 elapsed_time = tm_.gmtime(tm_.time() - start_time)