fixed save bug

CyXTraX/simulation/artist_bridge.py

@@ -63,8 +63,18 @@ class CylindricalProjection:
         temp_file = temp_file_path / f'temp_{GLOBAL_COUNTER:01}.tiff'
         GLOBAL_COUNTER += 1
         GLOBAL_COUNTER = GLOBAL_COUNTER % 10
+
         self.api.save_image(temp_file, save_projection_geometry=False, save_mode=SAVEMODES.FLOAT_TIFF)
         
+        while not temp_file.exists():
+            print('sleepy sleep sleep ...')
+            # The computation of the cylindrical xray tansforms takes time ... aRTist is not programmed for it.
+            # This catches problems with the computation and the remote control interfaces
+            # It is ugly ... but works ...
+            # Also if the mesh is not waterprof the triangle filter of artist seems to have problems.
+
+            sleep(2.)
+
         image = utility.load_projection(temp_file, load_projection_geometry=False)[0]
         os.remove(temp_file)
 

CyXTraX/util/datasets/augmentation_pipeline.py

+from jax import random, numpy as jnp
+
+class DataAugmentation:
+    def __init__(self, key: random.PRNGKey) -> None:
+        self._key = key
+        self.prost_process = list()
+
+    @property
+    def key(self) -> random.PRNGKey:
+        key2save, key2use = random.split(self._key)
+        self._key = key2save
+        return key2use
+    
+    def register(self):
+        pass
+    

CyXTraX/util/datasets/pipeline.py

@@ -5,6 +5,7 @@ from CyXTraX.io import record_atlas
 from jax import random, numpy as jnp
 from jax.scipy.spatial.transform import Rotation
 
+
 def generate_atlas_from_folder(
         folder: Path, key: random.PRNGKey,
         save_folder: Path,
@@ -28,3 +29,9 @@ def generate_atlas_from_folder(
                  stl_path.stem, save_folder,
                  map_bounding_box, number_of_maps)
     
+    
+    
+def merge_atlas_with_data_augmentation(folder: Path,
+                                       data_augmentation_pipeline):
+    
+    pass
\ No newline at end of file

scripts/06_generate_dataset.py

@@ -3,6 +3,11 @@ from pathlib import Path
 from jax import random
 
 
+"""
+This dataset adds 100 samples of random xray transforms.
+It takes about 300 minutes of time
+and needs 100gb of space.
+"""
 
 def main():
     # Dataset save folder
@@ -10,10 +15,11 @@ def main():
     # Dataset of multiple random stl files from: https://ten-thousand-models.appspot.com/
     load_folder = Path(r'C:\Users\swittl\Downloads\Thingi10K\Thingi10K\raw_meshes')
     
-    number_of_samples = len(list(save_folder.glob('*.stl')))
+    number_of_samples = len(list(save_folder.glob('*.h5'))) + 1
     
     for i in range(number_of_samples, number_of_samples + 100):
         # start from number of samples to generate diffrent rng keys!!!
+        print(i)
         key = random.PRNGKey(i)    
         generate_atlas_from_folder(
             load_folder, key, save_folder)