test(csps): fix and add tests, test data and baseline

Fixed typescript tests to properly compare json strings.

Added python tests for itkwasm-dicom-wasi and itkwasm-dicom-emscripten packages.

Added test and baseline datasets for dicom package.

Updated CI workflow to include installation of pillow
python dependency for itkwasm-dicom-wasi.

Author: jadh4v

.github/workflows/python-wasm.yml

@@ -143,6 +143,7 @@ jobs:
         if: ${{ matrix.python-minor-version < 10 }}
         working-directory: ./packages/dicom/python/itkwasm-dicom-wasi
         run: |
+          python -m pip install pillow
           python -m pip install -e .
           pytest
       - name: Test dicom-emscripten chrome

package.json

@@ -26,7 +26,7 @@
     "commit": "git cz",
     "bindgen": "node ./src/itk-wasm-cli.js bindgen ./dist/dicom/src ./dist/dicom/public/pipelines/*.wasm",
     "build": "npm run build:testData && npm run build:emscripten && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack && node ./src/io/internal/packages/package-json-gen.cjs && npm run build:emscripten:packages",
-    "build:testData": "dam download packages/dicom/test/data packages/dicom/test/data.tar.gz bafybeig4g7wosycckndpiouphtwowakccbkmunsvvgrg5bvjoz63p4s6hi https://w3s.link/ipfs/bafkreicrqj3nps6xep75zafmevtseitj6md2dgbce22jgizefuouc5vfca",
+    "build:testData": "dam download packages/dicom/test/data packages/dicom/test/data.tar.gz bafybeic2ckitzhl5b476fgfewt7ilel3mkzi5x66o6gga5s7n34g2t36xm https://w3s.link/ipfs/bafkreibxuanogkwccski66azxafdpjjj3sbua6g3pqdvwwwe72h3d6agoi",
     "build:debug": "npm run build:emscripten -- --debug && npm run build:tsc && npm run build:tscWorkersModuleLoader && npm run build:tscWebWorkers && npm run build:workerBundles && npm run build:workerMinBundles && npm run build:webpack -- --mode development",
     "build:tsc": "tsc --pretty",
     "build:tscWorkersModuleLoader": "tsc --types --lib es2017,webworker --rootDir ./src/ --outDir ./dist/ --moduleResolution node --target es2017 --module es2020 --strict --forceConsistentCasingInFileNames --declaration ./src/core/internal/loadEmscriptenModuleWebWorker.ts",

packages/dicom/python/itkwasm-dicom-emscripten/test/fixtures.py

@@ -17,8 +17,12 @@ def input_data():
     from pathlib import Path
     input_base_path = Path('..', '..', 'test', 'data')
     test_files = [
+        Path('input') / 'csps-input-image.dcm',
+        Path('input') / 'csps-input-pstate.dcm',
         Path('input') / 'gsps-pstate-test-input-image.dcm',
         Path('input') / 'gsps-pstate-test-input-pstate.dcm',
+        Path('baseline') / 'csps-pstate-baseline.json',
+        Path('baseline') / 'csps-output-image-baseline.bmp',
         Path('baseline') / 'gsps-pstate-baseline.json',
         Path('baseline') / 'gsps-pstate-image-baseline.pgm',
         Path('input') / '104.1-SR-printed-to-pdf.dcm',

packages/dicom/python/itkwasm-dicom-emscripten/test/test_apply_presentation_state_to_image_async.py

@@ -47,11 +47,74 @@ def write_input_data_to_fs(input_data, filename):
         # the slice operation removes the last EOF char from the baseline file.
         buffer = fp.read()[:-1]
     baseline_json_object = json.loads(buffer)
-    assert baseline_json_object['PresentationLabel'] == p_state_json_out['PresentationLabel']
-    assert baseline_json_object['PresentationSizeMode'] == p_state_json_out['PresentationSizeMode']
+
+    for key in baseline_json_object:
+        assert baseline_json_object[key] == p_state_json_out[key]
+
+    for key in p_state_json_out:
+        assert p_state_json_out[key] == baseline_json_object[key]
 
     baseline_image = 'gsps-pstate-image-baseline.pgm'
     baseline_buffer = input_data[baseline_image]
     # slice to get only the pixel buffer from the baseline image (pgm file)
     baseline_pixels = baseline_buffer[15:]
-    assert np.array_equal(np.frombuffer(baseline_pixels, dtype=np.uint8), output_image.data.ravel())
+    assert np.array_equal(np.frombuffer(baseline_pixels, dtype=np.uint8), output_image.data.ravel())
+
+@run_in_pyodide(packages=['micropip','pillow'])
+async def test_apply_color_presentation_state_to_dicom_image(selenium, package_wheel, input_data):
+    import json
+
+    import micropip
+    await micropip.install(package_wheel)
+    def write_input_data_to_fs(input_data, filename):
+        with open(filename, 'wb') as fp:
+            fp.write(input_data[filename])
+
+    from itkwasm_dicom_emscripten import apply_presentation_state_to_image_async
+    import numpy as np
+
+    input_file = 'csps-input-image.dcm'
+    write_input_data_to_fs(input_data, input_file)
+
+    p_state_file = 'csps-input-pstate.dcm'
+    write_input_data_to_fs(input_data, p_state_file)
+
+    from itkwasm.pyodide import to_js
+    p_state_json_out, output_image = await apply_presentation_state_to_image_async(input_file, p_state_file, color_output=True)
+
+    assert p_state_json_out != None
+    assert output_image != None
+
+    assert output_image.imageType.dimension == 2
+    assert output_image.imageType.componentType == 'uint8'
+    assert output_image.imageType.pixelType == 'RGB'
+    assert output_image.imageType.components == 3
+
+    assert np.array_equal(output_image.origin, [0, 0])
+    assert np.array_equal(output_image.spacing, [0.683, 0.683])
+    assert np.array_equal(output_image.direction, [[1, 0], [0, 1]])
+    assert np.array_equal(output_image.size, [768, 1024])
+
+    baseline_json_file = 'csps-pstate-baseline.json'
+    write_input_data_to_fs(input_data, baseline_json_file)
+    with open(baseline_json_file, 'r') as fp:
+        # the slice operation removes the last EOF char from the baseline file.
+        buffer = fp.read()[:-1]
+    baseline_json_object = json.loads(buffer)
+
+    for key in baseline_json_object:
+        assert baseline_json_object[key] == p_state_json_out[key]
+
+    for key in p_state_json_out:
+        assert p_state_json_out[key] == baseline_json_object[key]
+
+    baseline_image = 'csps-output-image-baseline.bmp'
+    write_input_data_to_fs(input_data, baseline_image)
+
+    from PIL import Image
+    im = Image.open(baseline_image)
+
+    baseline_pixels = np.array(im).flatten()
+    output_pixels = output_image.data.ravel().flatten()
+
+    assert np.array_equal(output_pixels, baseline_pixels)

packages/dicom/python/itkwasm-dicom-wasi/README.md

@@ -23,6 +23,7 @@ npm run build:testData
 cd -
 
 pip install pytest
+pip install pillow
 pip install -e .
 pytest
 # or

packages/dicom/python/itkwasm-dicom-wasi/pyproject.toml

@@ -34,7 +34,6 @@ requires-python = ">=3.7"
 dependencies = [
     "itkwasm >= 1.0.b105",
     "importlib_resources",
-
 ]
 
 [project.urls]
@@ -48,6 +47,7 @@ path = "itkwasm_dicom_wasi/_version.py"
 [tool.hatch.envs.default]
 dependencies = [
   "pytest",
+  "pillow",
 ]
 
 

packages/dicom/python/itkwasm-dicom-wasi/test/test_apply_presentation_state_to_image.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 import numpy as np
 import json
+from PIL import Image
 
 def test_apply_presentation_state_to_dicom_image():
     from itkwasm_dicom_wasi import apply_presentation_state_to_image
@@ -32,9 +33,12 @@ def test_apply_presentation_state_to_dicom_image():
         # the slice operation removes the last EOF char from the baseline file.
         buffer = fp.read()[:-1]
     baseline_json_object = json.loads(buffer)
-    assert baseline_json_object['PresentationLabel'] == p_state_json_out['PresentationLabel']
-    assert baseline_json_object['PresentationSizeMode'] == p_state_json_out['PresentationSizeMode']
-    assert str(baseline_json_object) == str(p_state_json_out)
+
+    for key in baseline_json_object:
+        assert baseline_json_object[key] == p_state_json_out[key]
+
+    for key in p_state_json_out:
+        assert p_state_json_out[key] == baseline_json_object[key]
 
     baseline_image = 'gsps-pstate-image-baseline.pgm'
     baseline_image_file_path = Path('..', '..', 'test', 'data', 'baseline', baseline_image)
@@ -58,3 +62,51 @@ def test_apply_presentation_state_to_dicom_image_input_does_not_exist():
         assert False
     except FileNotFoundError:
         pass
+
+def test_apply_color_presentation_state_to_dicom_image():
+    from itkwasm_dicom_wasi import apply_presentation_state_to_image
+
+    input_file = 'csps-input-image.dcm'
+    input_file_path = Path('..', '..', 'test', 'data', 'input', input_file)
+
+    p_state_file = 'csps-input-pstate.dcm'
+    p_state_file_path = Path('..', '..', 'test', 'data', 'input', p_state_file)
+
+    p_state_json_out, output_image = apply_presentation_state_to_image(input_file_path, p_state_file_path, color_output=True)
+
+    assert p_state_json_out != None
+    assert output_image != None
+
+    assert output_image.imageType.dimension == 2
+    assert output_image.imageType.componentType == 'uint8'
+    assert output_image.imageType.pixelType == 'RGB'
+    assert output_image.imageType.components == 3
+
+    assert np.array_equal(output_image.origin, [0, 0])
+    assert np.array_equal(output_image.spacing, [0.683, 0.683])
+    assert np.array_equal(output_image.direction, [[1, 0], [0, 1]])
+    assert np.array_equal(output_image.size, [768, 1024])
+
+    baseline_json_file = 'csps-pstate-baseline.json'
+    baseline_json_file_path = Path('..', '..', 'test', 'data', 'baseline', baseline_json_file)
+    with open(baseline_json_file_path, 'r') as fp:
+        # the slice operation removes the last EOF char from the baseline file.
+        buffer = fp.read()[:-1]
+    baseline_json_object = json.loads(buffer)
+
+    for key in baseline_json_object:
+        assert baseline_json_object[key] == p_state_json_out[key]
+
+    for key in p_state_json_out:
+        assert p_state_json_out[key] == baseline_json_object[key]
+
+    baseline_image = 'csps-output-image-baseline.bmp'
+    baseline_image_file_path = Path('..', '..', 'test', 'data', 'baseline', baseline_image)
+
+    from PIL import Image
+    im = Image.open(baseline_image_file_path)
+
+    baseline_pixels = np.array(im).flatten()
+    output_pixels = output_image.data.ravel().flatten()
+
+    assert np.array_equal(output_pixels, baseline_pixels)

packages/dicom/typescript/test/node.js

@@ -6,6 +6,7 @@ import {
   readDicomEncapsulatedPdfNode,
   applyPresentationStateToImageNode,
 } from '../dist/bundles/dicom-node.js'
+import { readImageLocalFile } from '../../../../dist/index.js'
 
   function arrayEquals(a, b) {
     return (a.length === b.length && a.every((val, idx) => val === b[idx]))
@@ -157,7 +158,7 @@ test('Apply presentation state to dicom image.', async t => {
 
   t.assert(baselineJsonObject.PresentationLabel === pstateJsonOut.PresentationLabel)
   t.assert(baselineJsonObject.PresentationSizeMode === pstateJsonOut.PresentationSizeMode)
-  t.assert(baselineJsonObject.toString() === pstateJsonOut.toString())
+  t.assert(JSON.stringify(baselineJsonObject) === JSON.stringify(pstateJsonOut))
 
   const baselineImage = 'gsps-pstate-image-baseline.pgm'
   const baselineImageFilePath = baselinePathPrefix + baselineImage
@@ -209,13 +210,11 @@ test('Apply color presentation state (CSPS) to a color dicom image.', async t =>
 
   t.assert(baselineJsonObject.PresentationLabel === pstateJsonOut.PresentationLabel)
   t.assert(baselineJsonObject.PresentationSizeMode === pstateJsonOut.PresentationSizeMode)
-  t.assert(baselineJsonObject.toString() === pstateJsonOut.toString())
+  t.assert(JSON.stringify(baselineJsonObject) === JSON.stringify(pstateJsonOut))
 
   const baselineImage = 'csps-output-image-baseline.bmp'
   const baselineImageFilePath = baselinePathPrefix + baselineImage
-  const baselineImageFileBuffer = fs.readFileSync(baselineImageFilePath)
-  // Slice to get only the pixel buffer from the baseline image (BMP file has 54 bytes of header data before pixel buffer begins).
-  const baselinePixels = baselineImageFileBuffer.slice(54)
-  t.assert(baselinePixels.length === outputImage.data.length)
-  t.assert(Buffer.compare(baselinePixels, outputImage.data) === 0)
+  const baselinePixels = await readImageLocalFile(baselineImageFilePath)
+  t.assert(baselinePixels.data.length === outputImage.data.length)
+  t.assert(Buffer.compare(baselinePixels.data, outputImage.data) === 0)
 })