Add 3 new demos using dicom (#24)

* Add ct scan data

* Update data

* Add mri examples

* Update CT data

* Add ct lung demo

* Update requirements for itk

* Apply black to demos

* Add dicom demos to tests

* Remove whole body data

* Update demos requirements

* Fix black version

* Add acknowledgements

* Add acknowledgements

Author: Xing Han Lu

.circleci/config.yml

@@ -24,6 +24,7 @@ jobs:
                 command: |
                     . venv/bin/activate
                     pip install --upgrade pip
+                    pip install black==20.8b1
                     pip install -r requirements.txt --quiet
                     pip install -r tests/requirements.txt --quiet
 

demos/data/citations.txt

@@ -0,0 +1,10 @@
+Pancreas MRI: 
+    Citation: Tatum, J., Kalen, J., Ileva, lilia, L, R., S, K., N, P., Jacobs, P., Sanders, C., A, J., Difilippantonio, S., L, T., hollingshead, melinda, J, P., Y, E., Clunie, D., Y, L., Suloway, C., Smith, K., U, W., … Doroshow, J. (n.d.). Imaging characterization of a metastatic patient derived model of adenocarcinoma pancreas: PDMR-292921-168-R. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2020.PCAK-8Z10
+
+Brain MRI:
+    URL: https://wiki.cancerimagingarchive.net/display/Public/Brain-Tumor-Progression
+    Citation: Schmainda KM, Prah M (2018). Data from Brain-Tumor-Progression. The Cancer Imaging Archive. http://doi.org/10.7937/K9/TCIA.2018.15quzvnb 
+
+Lung CT:
+    URL: https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=70224216#70224216bcab02c187174a288dbcbf95d26179e8
+    Citation: Li, P., Wang, S., Li, T., Lu, J., HuangFu, Y., & Wang, D. (2020). A Large-Scale CT and PET/CT Dataset for Lung Cancer Diagnosis [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/TCIA.2020.NNC2-0461

demos/data/ct_lung/1-01.dcm

@@ -0,0 +1,38 @@
+import os
+
+import dash
+import dash_html_components as html
+import itk
+
+import dash_vtk
+from dash_vtk.utils import to_volume_state
+
+# Place a DICOM series (a set of per-file slices) in a directory. ITK sorts, sets spatial metadata, etc.
+demo_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+itk_image = itk.imread(os.path.join(demo_dir, "data", "ct_lung"))
+
+# Convert itk.Image to vtkImageData
+vtk_image = itk.vtk_image_from_image(itk_image)
+volume_state = to_volume_state(vtk_image)
+
+
+vtk_view = dash_vtk.View(
+    dash_vtk.VolumeRepresentation(
+        children=[
+            dash_vtk.VolumeController(),
+            dash_vtk.Volume(state=volume_state),
+        ]
+    )
+)
+
+app = dash.Dash(__name__)
+server = app.server
+
+app.layout = html.Div(
+    style={"height": "calc(100vh - 50px)", "width": "100%"},
+    children=[html.Div(vtk_view, style={"height": "100%", "width": "100%"})],
+)
+
+
+if __name__ == "__main__":
+    app.run_server(debug=True)

demos/data/ct_lung/1-02.dcm

@@ -0,0 +1,6 @@
+# If you skipped `pip install -e ../../`, the package below will be retrieved from pypi:
+dash-vtk
+dash-bootstrap-components
+vtk
+numpy
+itk==5.2rc1

demos/data/ct_lung/1-03.dcm

@@ -0,0 +1,40 @@
+import os
+
+import dash
+import dash_html_components as html
+import dash_bootstrap_components as dbc
+import itk
+
+import dash_vtk
+from dash_vtk.utils import to_volume_state
+
+
+def dcm_to_volume(dir_path):
+    itk_image = itk.imread(dir_path)
+    vtk_image = itk.vtk_image_from_image(itk_image)
+    volume_state = to_volume_state(vtk_image)
+
+    return volume_state
+
+
+# Place a DICOM series (a set of per-file slices) in a directory. ITK sorts, sets spatial metadata, etc.
+demo_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+volume_state = dcm_to_volume(os.path.join(demo_dir, "data", "mri_brain"))
+
+app = dash.Dash(__name__)
+server = app.server
+
+vtk_view = dash_vtk.View(
+    dash_vtk.VolumeRepresentation(
+        [dash_vtk.VolumeController(), dash_vtk.Volume(state=volume_state)]
+    )
+)
+
+app.layout = html.Div(
+    style={"height": "calc(100vh - 50px)", "width": "100%"},
+    children=[html.Div(style={"height": "100%", "width": "100%"}, children=vtk_view)],
+)
+
+
+if __name__ == "__main__":
+    app.run_server(debug=True)

demos/data/ct_lung/1-04.dcm

@@ -0,0 +1,6 @@
+# If you skipped `pip install -e ../../`, the package below will be retrieved from pypi:
+dash-vtk
+dash-bootstrap-components
+vtk
+numpy
+itk==5.2rc1

demos/data/ct_lung/1-05.dcm

@@ -0,0 +1,40 @@
+import os
+
+import dash
+import dash_html_components as html
+import dash_bootstrap_components as dbc
+import itk
+
+import dash_vtk
+from dash_vtk.utils import to_volume_state
+
+
+def dcm_to_volume(dir_path):
+    itk_image = itk.imread(dir_path)
+    vtk_image = itk.vtk_image_from_image(itk_image)
+    volume_state = to_volume_state(vtk_image)
+
+    return volume_state
+
+
+# Place a DICOM series (a set of per-file slices) in a directory. ITK sorts, sets spatial metadata, etc.
+demo_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+volume_state = dcm_to_volume(os.path.join(demo_dir, "data", "mri_pancreas"))
+
+app = dash.Dash(__name__)
+server = app.server
+
+vtk_view = dash_vtk.View(
+    dash_vtk.VolumeRepresentation(
+        [dash_vtk.VolumeController(), dash_vtk.Volume(state=volume_state)]
+    )
+)
+
+app.layout = html.Div(
+    style={"height": "calc(100vh - 50px)", "width": "100%"},
+    children=[html.Div(style={"height": "100%", "width": "100%"}, children=vtk_view)],
+)
+
+
+if __name__ == "__main__":
+    app.run_server(debug=True)

demos/data/ct_lung/1-06.dcm

@@ -0,0 +1,6 @@
+# If you skipped `pip install -e ../../`, the package below will be retrieved from pypi:
+dash-vtk
+dash-bootstrap-components
+vtk
+numpy
+itk==5.2rc1

demos/data/ct_lung/1-07.dcm

@@ -68,7 +68,9 @@ def updateWarp(factor=1):
             ],
             colorMapPreset="erdc_blue2green_muted",
             colorDataRange=color_range,
-            property={"edgeVisibility": True,},
+            property={
+                "edgeVisibility": True,
+            },
         )
     ],
 )

demos/data/ct_lung/1-08.dcm

@@ -5,4 +5,7 @@
 -r ./volume-rendering/requirements.txt
 -r ./usage-vtk-cfd/requirements.txt
 -r ./usage-algorithm/requirements.txt
--r ./synthetic-volume-rendering/requirements.txt
+-r ./synthetic-volume-rendering/requirements.txt
+-r ./dicom-ct-lung/requirements.txt
+-r ./dicom-mri-brain/requirements.txt
+-r ./dicom-mri-pancreas/requirements.txt

demos/data/ct_lung/1-09.dcm

@@ -85,7 +85,11 @@
     children=[
         html.Div(
             style={"height": "20%", "display": "flex", "align-items": "center"},
-            children=[html.Br(), controls, html.Br(),],
+            children=[
+                html.Br(),
+                controls,
+                html.Br(),
+            ],
         ),
         html.Div(slice_view, style={"height": "80%"}),
     ],

demos/data/ct_lung/1-10.dcm

@@ -63,7 +63,10 @@
                 dbc.Col(
                     width=8,
                     children=[
-                        html.Div(vtk_view, style={"height": "100%", "width": "100%"},)
+                        html.Div(
+                            vtk_view,
+                            style={"height": "100%", "width": "100%"},
+                        )
                     ],
                 ),
             ],

demos/data/ct_lung/1-11.dcm

@@ -115,20 +115,36 @@ def getSeedState(self):
     children=[
         dash_vtk.GeometryRepresentation(
             id="bike-rep",
-            children=[dash_vtk.Mesh(id="bike", state=viz.getBikeMesh(),)],
+            children=[
+                dash_vtk.Mesh(
+                    id="bike",
+                    state=viz.getBikeMesh(),
+                )
+            ],
         ),
         dash_vtk.GeometryRepresentation(
             id="tubes-rep",
             colorMapPreset="erdc_rainbow_bright",
             colorDataRange=viz.getColorRange(),
-            children=[dash_vtk.Mesh(id="tubes-mesh", state=viz.getTubesMesh("p"),)],
+            children=[
+                dash_vtk.Mesh(
+                    id="tubes-mesh",
+                    state=viz.getTubesMesh("p"),
+                )
+            ],
         ),
         dash_vtk.GeometryRepresentation(
             id="seed-rep",
-            property={"color": [0.8, 0, 0], "representation": 0, "pointSize": 8,},
+            property={
+                "color": [0.8, 0, 0],
+                "representation": 0,
+                "pointSize": 8,
+            },
             children=[
                 dash_vtk.Algorithm(
-                    id="seed-line", vtkClass="vtkLineSource", state=viz.getSeedState(),
+                    id="seed-line",
+                    vtkClass="vtkLineSource",
+                    state=viz.getSeedState(),
                 )
             ],
         ),

demos/data/ct_lung/1-12.dcm

@@ -20,7 +20,10 @@
 
 vtk_view = dash_vtk.View(
     dash_vtk.VolumeRepresentation(
-        children=[dash_vtk.VolumeController(), dash_vtk.Volume(state=volume_state),]
+        children=[
+            dash_vtk.VolumeController(),
+            dash_vtk.Volume(state=volume_state),
+        ]
     )
 )
 

demos/data/ct_lung/1-13.dcm

@@ -19,8 +19,11 @@ def take_snapshot(dash_duo, name):
 names = [
     "usage",
     "demos.pyvista-terrain-following-mesh.app",
-    "demos.slice-rendering.app",
     "demos.pyvista-point-cloud.app",
+    "demos.dicom-ct-lung.app",
+    "demos.dicom-mri-brain.app",
+    "demos.dicom-mri-pancreas.app",
+    "demos.slice-rendering.app",
     "demos.volume-rendering.app",
     "demos.usage-vtk-cfd.app",
     "demos.usage-algorithm.app",