Merge pull request #8 from funkelab/v0.0.3

Add demo video and interactivity

MANIFEST.in

@@ -1,5 +1,3 @@
-include LICENSE
-include README.md
-
+include src/napari_cellulus/sample_data/*.npy
+include src/napari_cellulus/napari.yaml
 recursive-exclude * __pycache__
-recursive-exclude * *.py[co]

README.md

@@ -1,5 +1,8 @@
+
 <h2 align="center">A napari plugin for cellulus</h2>
 
+
+
 - **[Introduction](#introduction)**
 - **[Installation](#installation)**
 - **[Getting Started](#getting-started)**
@@ -55,8 +58,10 @@ Run the following commands in a terminal window:
 conda activate napari-cellulus
 napari
 ```
+[demo_cellulus.webm](https://github.com/funkelab/napari-cellulus/assets/34229641/35cb09de-c875-487d-9890-86082dcd95b2)
+
+
 
-Next, select `Cellulus` from the `Plugins` drop-down menu.
 
 ### Citation
 

setup.cfg

@@ -46,6 +46,10 @@ package_dir =
 [options.packages.find]
 where = src
 
+[options.package_data]
+napari_cellulus = *.npy
+* = *.yaml
+
 [options.entry_points]
 napari.manifest =
     napari-cellulus = napari_cellulus:napari.yaml
@@ -58,7 +62,3 @@ testing =
     pytest-qt  # https://pytest-qt.readthedocs.io/en/latest/
     napari
     pyqt5
-
-
-[options.package_data]
-* = *.yaml

src/napari_cellulus/__init__.py

@@ -1,5 +1,5 @@
 __version__ = "0.1.0"
 
-from .sample_data import tissue_net_sample
+from .load_sample_data import load_fluo_c2dl_huh7_sample
 
-__all__ = ("tissue_net_sample",)
+__all__ = ("load_fluo_c2dl_huh7_sample",)

src/napari_cellulus/datasets/napari_dataset.py

@@ -71,6 +71,7 @@ def __setup_pipeline(self):
                 )
                 + gp.Unsqueeze([self.raw], 0)
                 + gp.RandomLocation()
+                + gp.Normalize(self.raw, factor=self.normalization_factor)
             )
         else:
             self.pipeline = (
@@ -81,6 +82,7 @@ def __setup_pipeline(self):
                     spatial_dims=self.spatial_dims,
                 )
                 + gp.RandomLocation()
+                + gp.Normalize(self.raw, factor=self.normalization_factor)
             )
 
     def __iter__(self):
@@ -236,9 +238,20 @@ def sample_coordinates(self):
         return anchor_samples, reference_samples
 
     def get_num_anchors(self):
-        return int(
-            self.density * self.unbiased_shape[0] * self.unbiased_shape[1]
-        )
+        if self.num_spatial_dims == 2:
+            return int(
+                self.density * self.unbiased_shape[0] * self.unbiased_shape[1]
+            )
+        elif self.num_spatial_dims == 3:
+            return int(
+                self.density
+                * self.unbiased_shape[0]
+                * self.unbiased_shape[1]
+                * self.unbiased_shape[2]
+            )
 
     def get_num_references(self):
-        return int(self.density * self.kappa**2 * np.pi)
+        if self.num_spatial_dims == 2:
+            return int(self.density * np.pi * self.kappa**2)
+        elif self.num_spatial_dims == 3:
+            return int(self.density * 4 / 3 * np.pi * self.kappa**3)

src/napari_cellulus/datasets/napari_image_source.py

@@ -19,6 +19,7 @@ def __init__(
         self, image: Image, key: gp.ArrayKey, spec: ArraySpec, spatial_dims
     ):
         self.array_spec = spec
+
         self.image = gp.Array(
             data=normalize(
                 image.data.astype(np.float32), 1, 99.8, axis=spatial_dims

src/napari_cellulus/load_sample_data.py

@@ -0,0 +1,25 @@
+from pathlib import Path
+
+import numpy as np
+
+FLUO_C2DL_HUH7_SAMPLE_PATH = (
+    Path(__file__).parent / "sample_data/Fluo-C2DL-Huh7-sample.npy"
+)
+
+
+def load_fluo_c2dl_huh7_sample():
+    raw = np.load(FLUO_C2DL_HUH7_SAMPLE_PATH)
+    num_samples = raw.shape[0]
+    indices = np.random.choice(np.arange(num_samples), 5, replace=False)
+    raw = raw[indices]
+
+    return [
+        (
+            raw,
+            {
+                "name": "Raw",
+                "metadata": {"axes": ["s", "c", "y", "x"]},
+            },
+            "image",
+        )
+    ]

src/napari_cellulus/model.py

@@ -0,0 +1,48 @@
+import torch
+
+
+class Model(torch.nn.Module):
+    """
+    This class is a wrapper on the model object returned by cellulus.
+    It updates the `forward` function and handles cases when the input raw
+    image is not (S, C, (Z), Y, X) type.
+    """
+
+    def __init__(self, model, selected_axes):
+        super().__init__()
+        self.model = model
+        self.selected_axes = selected_axes
+
+    def forward(self, raw):
+        if "s" in self.selected_axes and "c" in self.selected_axes:
+            pass
+        elif "s" in self.selected_axes and "c" not in self.selected_axes:
+
+            raw = torch.unsqueeze(raw, 1)
+        elif "s" not in self.selected_axes and "c" in self.selected_axes:
+            pass
+        elif "s" not in self.selected_axes and "c" not in self.selected_axes:
+            raw = torch.unsqueeze(raw, 1)
+        return self.model(raw)
+
+    @staticmethod
+    def select_and_add_coordinates(outputs, coordinates):
+        selections = []
+        # outputs.shape = (b, c, h, w) or (b, c, d, h, w)
+        for output, coordinate in zip(outputs, coordinates):
+            if output.ndim == 3:
+                selection = output[:, coordinate[:, 1], coordinate[:, 0]]
+            elif output.ndim == 4:
+                selection = output[
+                    :, coordinate[:, 2], coordinate[:, 1], coordinate[:, 0]
+                ]
+            selection = selection.transpose(1, 0)
+            selection += coordinate
+            selections.append(selection)
+
+        # selection.shape = (b, c, p) where p is the number of selected positions
+        return torch.stack(selections, dim=0)
+
+    def set_infer(self, p_salt_pepper, num_infer_iterations, device):
+        self.model.eval()
+        self.model.set_infer(p_salt_pepper, num_infer_iterations, device)

src/napari_cellulus/napari.yaml

@@ -1,23 +1,17 @@
 name: napari-cellulus
-display_name: Cellulus
+display_name: napari-cellulus
 contributions:
   commands:
-    - id: napari-cellulus.tissue_net_sample
-      python_name: napari_cellulus.sample_data:tissue_net_sample
-      title: Load sample data from Cellulus
-    - id: napari-cellulus.fluo_n2dl_hela_sample
-      python_name: napari_cellulus.sample_data:fluo_n2dl_hela_sample
-      title: Load sample data from Cellulus
+    - id: napari-cellulus.load_fluo_c2dl_huh7_sample
+      python_name: napari_cellulus.load_sample_data:load_fluo_c2dl_huh7_sample
+      title: Load sample data
     - id: napari-cellulus.Widget
       python_name: napari_cellulus.widget:Widget
       title: Cellulus
   sample_data:
-    - command: napari-cellulus.tissue_net_sample
-      display_name: TissueNet
-      key: tissue_net_sample
-    - command: napari-cellulus.fluo_n2dl_hela_sample
-      display_name: Fluo-N2DL-HeLa
-      key: fluo_n2dl_hela_sample
+    - command: napari-cellulus.load_fluo_c2dl_huh7_sample
+      display_name: Fluo-C2DL-Huh7
+      key: load_fluo_c2dl_huh7_sample
   widgets:
     - command: napari-cellulus.Widget
       display_name: Cellulus