Export packing outputs as a tiff file (#166)

* refactor loops over ingredients and compartments in ImageWriter

* linting

* formatting with black

* remove duplicated image export

cellpack/autopack/Analysis.py

@@ -35,7 +35,6 @@
 from cellpack.autopack.upy.colors import map_colors
 from cellpack.autopack.utils import check_paired_key, get_paired_key
 from cellpack.autopack.writers.ImageWriter import ImageWriter
-
 import concurrent.futures
 import multiprocessing
 

cellpack/autopack/Environment.py

@@ -585,7 +585,8 @@ def save_result(
 
         self.log.info("time to save result file %d", time() - t0)
         if vAnalysis == 1:
-            # START Analysis Tools: Graham added back this big chunk of code for analysis tools and graphic on 5/16/12
+            # START Analysis Tools: Graham added back this big chunk of code
+            # for analysis tools and graphic on 5/16/12
             # Needs to be cleaned up into a function and proper uPy code
             # totalVolume = self.grid.gridVolume*unitVol
             unitVol = self.grid.gridSpacing**3
@@ -754,8 +755,9 @@ def save_result(
             self.log.info("self.gridVolume = %d", self.grid.gridVolume)
             self.log.info("histoVol.timeUpDistLoopTotal = %d", self.timeUpDistLoopTotal)
 
-            # END Analysis Tools: Graham added back this big chunk of code for analysis tools and graphic on 5/16/12
-            # Needs to be cleaned up into a function and proper uPy code
+            #    END Analysis Tools: Graham added back this big chunk of code
+            #  for analysis tools and graphic on 5/16/12
+            #  Needs to be cleaned up into a function and proper uPy code
         self.log.info("time to save end %d", time() - t0)
 
     def loadResult(
@@ -1392,7 +1394,6 @@ def buildGrid(self, rebuild=True):
         if self.previous_grid_file is not None:
             distance = self.grid.distToClosestSurf  # [:]
             nbFreePoints = nbPoints  # -1
-            # Graham turned this off on 5/16/12 to match August Repair for May Hybrid
             for i, mingrs in enumerate(
                 self.molecules
             ):  # ( jtrans, rotMatj, self, ptInd )
@@ -1724,8 +1725,9 @@ def pickIngredient(self, vThreshStart, verbose=0):
                 ingr = self.activeIngr[0]
             else:
                 # prob = uniform(vRangeStart,1.0)
-                # Graham 9/21/11 This is wrong...vRangeStart is the point index,
-                # need active list i.e. thresholdPriority to be limited
+                # #Graham 9/21/11 This is wrong...
+                # vRangeStart is the point index, need active list
+                # i.e. thresholdPriority to be limited
                 prob = uniform(0, 1.0)
                 ingrInd = 0
                 for threshProb in self.thresholdPriorities:
@@ -3350,3 +3352,68 @@ def applyStep(self, step):
         # if self.traj.traj_type=="dcd" or self.traj.traj_type=="xyz":
         self.traj.applyState_primitive_name(self, step)
         # ho can we apply to parent instance the rotatiotn?
+
+    def create_voxelization(self, image_data, image_size, voxel_size, hollow=False):
+        """
+        Update the image data for all molecules in the recipe by creating voxelized
+        representations.
+
+        Parameters
+        ----------
+        image_data: numpy.ndarray
+            The image data to update.
+        image_size: list
+            The size of the image data.
+        voxel_size: float
+            The size of a voxel in the image data.
+        hollow: bool
+            If True, the voxelization will be hollow.
+
+        Returns
+        ----------
+        image_data: numpy.ndarray
+            The updated image data.
+        """
+        channel_colors = []
+        for pos, rot, ingr, _ in self.molecules:
+            if ingr.name not in image_data:
+                image_data[ingr.name] = numpy.zeros(image_size, dtype=numpy.uint8)
+                if ingr.color is not None:
+                    color = ingr.color
+                    if all([x <= 1 for x in ingr.color]):
+                        color = [int(col * 255) for col in ingr.color]
+                    channel_colors.append(color)
+
+            image_data[ingr.name] = ingr.create_voxelization(
+                image_data=image_data[ingr.name],
+                bounding_box=self.boundingBox,
+                voxel_size=voxel_size,
+                image_size=image_size,
+                position=pos,
+                rotation=rot,
+            )
+
+        for compartment in self.compartments:
+            if compartment.name not in image_data:
+                image_data[compartment.name] = numpy.zeros(
+                    image_size, dtype=numpy.uint8
+                )
+                if hasattr(compartment, "color") and compartment.color is not None:
+                    color = compartment.color
+                    if all([x <= 1 for x in compartment.color]):
+                        color = [int(col * 255) for col in compartment.color]
+                    channel_colors.append(color)
+                else:
+                    channel_colors.append([0, 255, 0])
+
+            image_data[compartment.name] = compartment.create_voxelization(
+                image_data=image_data[compartment.name],
+                bounding_box=self.boundingBox,
+                voxel_size=voxel_size,
+                image_size=image_size,
+                position=compartment.position,
+                mesh_store=self.mesh_store,
+                hollow=hollow,
+            )
+
+        return image_data, channel_colors

cellpack/autopack/writers/ImageWriter.py

@@ -178,50 +178,10 @@ def create_voxelization(self):
         """
         Creates a voxelized representation of the current scene
         """
-        channel_colors = []
-
-        for pos, rot, ingr, _ in self.env.molecules:
-            if ingr.name not in self.image_data:
-                self.image_data[ingr.name] = numpy.zeros(
-                    self.image_size, dtype=numpy.uint8
-                )
-                if ingr.color is not None:
-                    color = ingr.color
-                    if all([x <= 1 for x in ingr.color]):
-                        color = [int(col * 255) for col in ingr.color]
-                    channel_colors.append(color)
-
-            self.image_data[ingr.name] = ingr.create_voxelization(
-                image_data=self.image_data[ingr.name],
-                bounding_box=self.env.boundingBox,
-                voxel_size=self.voxel_size,
-                image_size=self.image_size,
-                position=pos,
-                rotation=rot,
-            )
 
-        for compartment in self.env.compartments:
-            if compartment.name not in self.image_data:
-                self.image_data[compartment.name] = numpy.zeros(
-                    self.image_size, dtype=numpy.uint8
-                )
-                if hasattr(compartment, "color") and compartment.color is not None:
-                    color = compartment.color
-                    if all([x <= 1 for x in compartment.color]):
-                        color = [int(col * 255) for col in compartment.color]
-                    channel_colors.append(color)
-                else:
-                    channel_colors.append([0, 255, 0])
-
-            self.image_data[compartment.name] = compartment.create_voxelization(
-                image_data=self.image_data[compartment.name],
-                bounding_box=self.env.boundingBox,
-                voxel_size=self.voxel_size,
-                image_size=self.image_size,
-                position=compartment.position,
-                mesh_store=self.env.mesh_store,
-                hollow=self.hollow,
-            )
+        self.image_data, channel_colors = self.env.create_voxelization(
+            self.image_data, self.image_size, self.voxel_size, self.hollow
+        )
 
         concatenated_image = numpy.zeros(
             (len(self.image_data), *self.image_size), dtype=numpy.uint8

cellpack/tests/packing-configs/test_image_config.json

@@ -0,0 +1,30 @@
+{
+    "name": "test_image_config_convolved",
+    "format": "simularium",
+    "inner_grid_method": "trimesh",
+    "live_packing": false,
+    "ordered_packing": false,
+    "out": "out/",
+    "overwrite_place_method": true,
+    "place_method": "spheresSST",
+    "save_analyze_result": true,
+    "show_grid_plot": true,
+    "number_of_packings": 1,
+    "spacing": null,
+    "use_periodicity": false,
+    "show_sphere_trees": false,
+    "load_from_grid_file": true,
+    "save_converted_recipe": true,
+    "image_export_options": {
+        "hollow": false,
+        "voxel_size": [1,1,1],
+        "projection_axis": "z",
+        "convolution_options": {
+            "psf": "gaussian",
+            "psf_parameters":{
+                "sigma": 2,
+                "size": [5,5,5]
+            }
+        }
+    }
+}