Merge pull request #82 from MPI-Dortmund/write_positions_into_umap

Write umap embeddings metadata + positions  into umap attrs and remove label mask calculation

tomotwin/modules/tools/umap.py

@@ -9,7 +9,6 @@
 except ImportError:
     print("cuml can't be loaded")
 
-import mrcfile
 import numpy as np
 import pandas as pd
 from numpy.typing import ArrayLike
@@ -98,28 +97,6 @@ def calcuate_umap(
 
         return embedding, reducer
 
-    def create_embedding_mask(self, embeddings: pd.DataFrame):
-        """
-        Creates mask where each individual subvolume of the running windows gets an individual ID
-        """
-        print("Create embedding mask")
-        Z = embeddings.attrs["tomogram_input_shape"][0]
-        Y = embeddings.attrs["tomogram_input_shape"][1]
-        X = embeddings.attrs["tomogram_input_shape"][2]
-        stride = embeddings.attrs["stride"][0]
-        segmentation_array = np.zeros(shape=(Z, Y, X), dtype=np.float32)
-        z = np.array(embeddings["Z"], dtype=int)
-        y = np.array(embeddings["Y"], dtype=int)
-        x = np.array(embeddings["X"], dtype=int)
-
-        values = np.array(range(1, len(x) + 1))
-        for stride_x in tqdm(list(range(stride))):
-            for stride_y in range(stride):
-                for stride_z in range(stride):
-                    index = (z + stride_z, y + stride_y, x + stride_x)
-                    segmentation_array[index] = values
-
-        return segmentation_array
 
     def run(self, args):
         print("Read data")
@@ -144,23 +121,18 @@ def run(self, args):
         os.makedirs(out_pth,exist_ok=True)
         fname = os.path.splitext(os.path.basename(args.input))[0]
         df_embeddings = pd.DataFrame(umap_embeddings)
+        df_embeddings.reset_index(drop=True, inplace=True)
+        embeddings.reset_index(drop=True, inplace=True)
 
         print("Write embeedings to disk")
         df_embeddings.columns = [f"umap_{i}" for i in range(umap_embeddings.shape[1])]
+        df_embeddings = pd.concat([embeddings[['X', 'Y', 'Z']], df_embeddings], axis=1)
+        df_embeddings.attrs['embeddings_attrs'] = embeddings.attrs
+        df_embeddings.attrs['embeddings_path'] = os.path.realpath(args.input)
+
         df_embeddings.to_pickle(os.path.join(out_pth,fname+".tumap"))
 
         print("Write umap model to disk")
         pickle.dump(fitted_umap, open(os.path.join(out_pth, fname + "_umap_model.pkl"), "wb"))
 
-        print("Calculate label mask and write it to disk")
-        embedding_mask = self.create_embedding_mask(embeddings)
-        with mrcfile.new(
-                os.path.join(
-                    args.output,
-                    fname + "_label_mask.mrci",
-                ),
-                overwrite=True,
-        ) as mrc:
-            mrc.set_data(embedding_mask)
-
         print("Done")