[91] - Adding CT loading functionality to web interface (#161)

* Adding CT loading functionality to web

* Fixing issues with ct loading

* Adding support to load zipped dicom CTs

* Spellcheck

* Adding absorption to shaped grid

* Exposing CT scan info to the FE, so that we can make FE validations

* Constraining the distance from origin based on the CT size

* Removing unused pynrrd lib

* Small refactoring

* Refactoring

* Using voxels spacing when creating the grid

* Adding dependency

* Reverting the X/Y swap

* Removing gunicorn and replacing the make tarket web with web-development

* Pin stride version in all the places we specify pip install (#163)

* Pin stride version in all the places we specify pip install
* Fix dead link

* Poetry version updated

* Add focal pressure, focal volume, and FWHM to results metrics (#152)

* Poetry version updated

---------

Co-authored-by: newton sander <[email protected]>
Co-authored-by: charles <[email protected]>
Co-authored-by: d-lucena <[email protected]>

Makefile

@@ -1,7 +1,7 @@
-.PHONY:help lint lint-check test test-coverage test-unit test-integration docs web web-development
+.PHONY:help lint lint-check test test-coverage test-unit test-integration docs web
 
 help:
-	@echo "Available commands are: \n*lint, lint-check, spellcheck, test, test-unit, test-integration docs web web-development"
+	@echo "Available commands are: \n*lint, lint-check, spellcheck, test, test-unit, test-integration docs web"
 
 lint:
 	poetry run isort src tests docs/examples
@@ -46,8 +46,5 @@ test-integration:
 docs:
 	poetry run mkdocs build
 
-web-development:
-	poetry run ndk-ui
-
 web:
-	poetry run gunicorn -b 0.0.0.0 -w 1 --timeout 99999999 'src.web.app:app'
+	poetry run ndk-ui

docs/user_interface.md

@@ -33,7 +33,7 @@ There are multiple ways of running the web server, you can choose between:
 1. Open a terminal in the project location and run the following command
 
     ```
-    make web-development
+    make web
     ```
 
 ### Docker

pyproject.toml

@@ -43,8 +43,9 @@ mkdocs-gallery = "0.7.6"
 xarray = ">=2022.3.0"
 flask = {extras = ["async"], version = "^2.3.3"}
 pydantic = "<2"
-gunicorn = "^21.2.0"
 pyrevolve = ">=2.2.3"
+pydicom = "^2.4.3"
+nibabel = "^5.1.0"
 
 [tool.poetry.group.dev.dependencies]
 black = {extras = ["jupyter"], version = "^23.9.1"}

src/neurotechdevkit/grid.py

@@ -34,20 +34,45 @@ class Grid(stride.Grid):
 
     @staticmethod
     def make_shaped_grid(
-        shape: Tuple[int, int],
-        spacing: float,
+        shape: Tuple[int, ...],
+        spacing: Union[float, Tuple[float, ...]],
+        extra: Union[int, Iterable[int]] = 50,
+        absorbing: Union[int, Iterable[int]] = 40,
     ) -> "Grid":
-        """Create an NDK Grid with the given shape.
+        """Create an NDK Grid with a given shape.
+
+        Note that the time component of the grid is not defined here. That is
+        created at simulation time because it depends on simulation parameters.
 
         Args:
-            shape: a tuple of two integers representing the shape of the grid.
+            shape: a tuple of integers representing the shape of the grid.
             spacing: a float representing the axis-wise spacing of the grid, in
                 meters.
+            extra: an integer or an iterable of integers representing the number
+                of gridpoints to add as boundary layers on each side of the grid.
+                Extras are added both before and after the grid on each axis.
+                Default is 50.
+            absorbing: an integer or an iterable of integers representing the
+                number of gridpoints within the boundary layers that are
+                absorbing. Default is 40.
 
         Returns:
             Grid: the Grid object.
         """
-        space = stride.Space(shape=shape, spacing=spacing)
+        n_dims = len(shape)
+
+        if isinstance(extra, int):
+            extra = (extra,) * n_dims
+        else:
+            extra = tuple(extra)
+        if isinstance(absorbing, int):
+            absorbing = (absorbing,) * n_dims
+        else:
+            absorbing = tuple(absorbing)
+
+        space = stride.Space(
+            shape=shape, extra=extra, absorbing=absorbing, spacing=spacing
+        )
         return Grid(space=space, time=None)
 
     @staticmethod
@@ -84,18 +109,7 @@ def make_grid(
             Grid: the Grid object.
         """
         _extent = np.array(extent, dtype=float)
-        n_dims = len(_extent)
         dx = speed_water / center_frequency / ppw  # m
         shape = _compute_grid_shape(_extent, dx)
 
-        if isinstance(extra, int):
-            extra = (extra,) * n_dims
-        else:
-            extra = tuple(extra)
-        if isinstance(absorbing, int):
-            absorbing = (absorbing,) * n_dims
-        else:
-            absorbing = tuple(absorbing)
-
-        space = stride.Space(shape=shape, extra=extra, absorbing=absorbing, spacing=dx)
-        return Grid(space=space, time=None)
+        return Grid.make_shaped_grid(shape, dx, extra, absorbing)

src/neurotechdevkit/scenarios/built_in/_scenario_2.py

@@ -365,7 +365,7 @@ def _create_scenario_2_mask(
         brain_mask = brain_mask[:, :, z_center_idx]
 
     if skull_mask.shape != output_shape:
-        # resample the mask to match the grid
+        # re-sample the mask to match the grid
         scale_factor = np.array(output_shape) / np.array(skull_mask.shape)
         skull_mask = scipy.ndimage.zoom(skull_mask, scale_factor, order=0)
         brain_mask = scipy.ndimage.zoom(brain_mask, scale_factor, order=0)

src/web/app.py

@@ -1,9 +1,14 @@
 """Flask app factory."""
+import os
+import pathlib
+
 import matplotlib
 from flask import Flask
 from matplotlib import rc
 from web.simulation_runner import SimulationRunner
 
+CT_FOLDER = pathlib.Path("./ct-scans/")
+
 
 def create_app():
     """Create the Flask app."""
@@ -23,11 +28,19 @@ def create_app():
     return app
 
 
+def assign_CT_FOLDER(app):
+    """Assign the CT_FOLDER to the app."""
+    if not os.path.exists(CT_FOLDER):
+        os.makedirs(CT_FOLDER)
+    app.config["CT_FOLDER"] = CT_FOLDER
+
+
 app = create_app()
 
 
 def run():
     """Run the web app."""
+    assign_CT_FOLDER(app)
     app.run(host="0.0.0.0", port=5000, debug=True)