feat: Initial test scenario

.devcontainer/Dockerfile

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+FROM ubuntu:noble-20240429 AS build
+
+RUN apt-get update && apt install -y python3-all pip git
+RUN apt-get update && apt install -y python3-pandas python3-openpyxl

.devcontainer/devcontainer.json

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+// For format details, see https://aka.ms/vscode-remote/devcontainer.json or this file's README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.117.1/containers/cpp
+{
+	// docker run   your_image_name
+	"name": "C++",
+	"dockerFile": "./Dockerfile",
+	"mounts": [
+		{
+			"source": "/home/joachim-danmayr/Documents/github/conan_cache",
+			"target": "/root/.conan2",
+			"type": "bind"
+		}
+	],
+	"runArgs": [],
+	"customizations": {
+		// Set *default* container specific settings.json values on container create.
+		"settings": {
+			"terminal.integrated.shell.linux": "/bin/sh"
+		},
+		// Add the IDs of extensions you want installed when the container is created.
+		"vscode": {
+			"extensions": [
+				"ms-vscode.cpptools",
+				"llvm-vs-code-extensions.vscode-clangd",
+				"GrapeCity.gc-excelviewer",
+				"streetsidesoftware.code-spell-checker",
+				"vscjava.vscode-java-pack",
+				"xaver.clang-format",
+				"felgo.felgo"
+			]
+		}
+	}
+}

.github/CODEOWNERS

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+@joda01

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for more information:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# https://containers.dev/guide/dependabot
+
+version: 2
+updates:
+ - package-ecosystem: "devcontainers"
+   directory: "/"
+   schedule:
+     interval: weekly

.github/workflows/run-test.yml

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+name: imagec-test
+
+on:
+  push:
+    branches:
+      - main
+      - init
+
+jobs:
+  prepare-test:
+    runs-on: self-hosted
+    steps:
+      - uses: actions/checkout@v4
+      - run: |
+          echo "Download latest ImageC ..."
+#          ./prepare_test_bench.sh /home/actions-runner/test_data
+#          echo "Run test ..."
+#          ./run_test.sh /home/actions-runner/test_data

.gitignore

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+/imagec-x64-linux
+/tmp
+/test_data
+/scenarios/*/results
+/scenarios/*/models

.vscode/launch.json

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+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+
+        {
+            "name": "Python Debugger: run test",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "run_test.py",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "./tmp/",
+                "./ref_exports/"
+            ]
+        },
+        {
+            "name": "Python Debugger: Current File",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+        }
+
+    ]
+}

.vscode/settings.json

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+{
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        ".",
+        "-p",
+        "test*.py"
+    ],
+    "python.testing.pytestEnabled": false,
+    "python.testing.unittestEnabled": true
+}

README.md

@@ -1,2 +1,17 @@
 # imagec-test
-Automatic test execution for ImageC
+TODO:
+* add dockerfile to repository
+* add to dockerfile: pip install unittest-xml-reporting (v3.2)
+
+1) Download `test_data.zip` and extract to project folder
+2) Execute `prepare_test_bench.sh` which downloads the latest ImageC version and copy the AI model paths to the ImageC folder
+3) Execute `run_test.sh` to run the tests.
+4) If you want to create new reference export files: execute `run_export.sh --ref`. This will copy the reference export files to the
+folder /ref_exports
+
+Open problems:
+* The dataset contains one plate with 2 wells (A5 and A6). During the analysis the assignment of the group_id is arbitrary, either group_id=0 for A5 and group_id=1 for A6, or vice versa. 
+* As the group_id is also used for export, the export for group_id=0 could be well A5 or A6.
+* For the ref_exports group_id=0 is used for A5, group_id=1 for A6.
+* If the group_ids match there are 4 files with differences. It always concerns dapi_mb@spot-Intensity avg[]
+

compare_excel_files.py

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+import os
+import sys
+import pandas as pd
+import numpy as np
+
+
+def normalize_and_compare(df1, df2, tol=1e-6):
+    # Check shape and column names
+    if df1.shape[1] != df2.shape[1] or list(df1.columns) != list(df2.columns):
+        return False, "Shape or column mismatch"
+
+    diff_mask = pd.DataFrame(False, index=df1.index, columns=df1.columns)
+
+    for col in df1.columns:
+        # Skip cell comparison for "Object ID" columns
+        if "object id" in col.lower():
+            continue  
+
+        s1 = df1[col]
+        s2 = df2[col]
+
+        if pd.api.types.is_numeric_dtype(s1) and pd.api.types.is_numeric_dtype(s2):
+            equal = np.isclose(s1.fillna(np.nan), s2.fillna(np.nan), atol=tol, equal_nan=True)
+            diff_mask[col] = ~equal
+        else:
+            equal = (s1.fillna("").astype(str).str.strip() ==
+                     s2.fillna("").astype(str).str.strip())
+            diff_mask[col] = ~equal
+
+    is_equal = not diff_mask.any().any()
+    return is_equal, diff_mask
+
+
+def detailed_diff_report(df1, df2, diff_mask, sheet_name):
+    print(f"     ➤ Differences found in sheet '{sheet_name}':")
+    rows, cols = np.where(diff_mask.to_numpy())
+    for r, c in zip(rows, cols):
+        col_name = df1.columns[c]
+        # Skip reporting "Object ID" differences (already excluded)
+        if "object id" in col_name.lower():
+            continue
+        val1 = df1.iat[r, c]
+        val2 = df2.iat[r, c]
+        print(f"       - Row {r+1}, Column '{col_name}': file1 = '{val1}' vs file2 = '{val2}'")
+
+
+def compare_excel_files(folder1, folder2, tol=1e-6):
+    has_difference = False
+
+    files1 = set(f for f in os.listdir(folder1) if f.endswith('.xlsx'))
+    files2 = set(f for f in os.listdir(folder2) if f.endswith('.xlsx'))
+    all_files = sorted(files1 | files2)
+
+    for filename in all_files:
+        path1 = os.path.join(folder1, filename)
+        path2 = os.path.join(folder2, filename)
+
+        print(f"\n📄 Comparing file: {filename}")
+
+        if filename not in files1:
+            print(f"  ❌ Missing in folder1: {filename}")
+            has_difference = True
+            continue
+        if filename not in files2:
+            print(f"  ❌ Missing in folder2: {filename}")
+            has_difference = True
+            continue
+
+        try:
+            excel1 = pd.ExcelFile(path1)
+            excel2 = pd.ExcelFile(path2)
+
+            sheets1 = excel1.sheet_names
+            sheets2 = excel2.sheet_names
+
+            if set(sheets1) != set(sheets2):
+                print("  ❗ Sheet names differ:")
+                print("   ➤ Only in folder1:", set(sheets1) - set(sheets2))
+                print("   ➤ Only in folder2:", set(sheets2) - set(sheets1))
+                has_difference = True
+
+            # Skip first sheet
+            common_sheets = sorted(set(sheets1[1:]) & set(sheets2[1:]))
+
+            for sheet in common_sheets:
+                df1 = excel1.parse(sheet)
+                df2 = excel2.parse(sheet)
+
+                equal, result = normalize_and_compare(df1, df2, tol=tol)
+
+                if equal:
+                    print(f"  ✅ Sheet '{sheet}' is identical (within tol={tol}).")
+                else:
+                    print(f"  ❌ Sheet '{sheet}' differs:")
+                    has_difference = True
+                    if isinstance(result, str):
+                        print(f"     ➤ {result}")
+                    else:
+                        detailed_diff_report(df1, df2, result, sheet)
+
+        except Exception as e:
+            print(f"  ⚠️ Error processing {filename}: {e}")
+            has_difference = True
+
+    return 1 if has_difference else 0
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 3:
+        print("Usage: python compare_excel_files.py <folder1> <folder2>")
+        sys.exit(1)
+
+    folder1 = sys.argv[1]
+    folder2 = sys.argv[2]
+
+    if not os.path.isdir(folder1):
+        print(f"❌ Folder not found: {folder1}")
+        sys.exit(1)
+    if not os.path.isdir(folder2):
+        print(f"❌ Folder not found: {folder2}")
+        sys.exit(1)
+
+    exit_code = compare_excel_files(folder1, folder2, tol=1e-6)
+    sys.exit(exit_code)

old/run_export.sh

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+
+
+#
+# Execute the analysis
+#
+run_analyze_scenario_01(){
+  QT_QPA_PLATFORM="offscreen"
+  export QT_QPA_PLATFORM
+  MY_PATH=$PWD
+  SCENARIO_PATH="$MY_PATH/scenarios/scenario_01"
+  cd imagec-x64-linux
+  rm -rf ${MY_PATH}/test_data/test_images_v1/imagec
+  ./imagec.sh --run ${SCENARIO_PATH}/scenario_v1.icproj --run-path ${MY_PATH}/test_data/test_images_v1
+  cd ..
+}
+
+#
+# Run the unit test
+# runs only outside docker
+#
+run_export_files_01(){
+  image_names=(
+    B2_15_5ADVMLE.vsi.vsi
+    B4_15_5ADVMLE.vsi.vsi  
+    B8_15_5ADVMLE.vsi.vsi
+    B2_16_5ADVMLE.vsi.vsi
+    B4_16_5ADVMLE.vsi.vsi
+    B8_16_5ADVMLE.vsi.vsi
+  )
+  QT_QPA_PLATFORM="offscreen"
+  export QT_QPA_PLATFORM
+  MY_PATH=$PWD
+  rm -rf $MY_PATH/$TARGET_FOLDER
+  mkdir -p $MY_PATH/$TARGET_FOLDER 
+  SCENARIO_PATH="$MY_PATH/scenarios/scenario_01"
+  cd imagec-x64-linux
+  #cd /home/manfred/Documents/imagec-x64-linux-bundle/imagec-x64-linux
+  ./imagec.sh --export ${MY_PATH}/test_data/test_images_v1/imagec/*/results.icdb --export-output $MY_PATH/$TARGET_FOLDER/plate.xlsx --export-columns ${SCENARIO_PATH}/export_scenario_v1.ictemplexp --export-type xlsx --export-format list --export-view plate --export-filter "1 0"
+  ./imagec.sh --export ${MY_PATH}/test_data/test_images_v1/imagec/*/results.icdb --export-output $MY_PATH/$TARGET_FOLDER/well_0.xlsx --export-columns ${SCENARIO_PATH}/export_scenario_v1.ictemplexp --export-type xlsx --export-format list --export-view well --export-filter "1 0"
+  ./imagec.sh --export ${MY_PATH}/test_data/test_images_v1/imagec/*/results.icdb --export-output $MY_PATH/$TARGET_FOLDER/well_1.xlsx --export-columns ${SCENARIO_PATH}/export_scenario_v1.ictemplexp --export-type xlsx --export-format list --export-view well --export-filter "1 1"
+  ./imagec.sh --export ${MY_PATH}/test_data/test_images_v1/imagec/*/results.icdb --export-output $MY_PATH/$TARGET_FOLDER/plate_heatmap.xlsx --export-columns ${SCENARIO_PATH}/export_scenario_v1.ictemplexp --export-type xlsx --export-format heatmap --export-view plate --export-filter "1 0"
+  ./imagec.sh --export ${MY_PATH}/test_data/test_images_v1/imagec/*/results.icdb --export-output $MY_PATH/$TARGET_FOLDER/well_0_heatmap.xlsx --export-columns ${SCENARIO_PATH}/export_scenario_v1.ictemplexp --export-type xlsx --export-format heatmap --export-view well --export-filter "1 0"
+  ./imagec.sh --export ${MY_PATH}/test_data/test_images_v1/imagec/*/results.icdb --export-output $MY_PATH/$TARGET_FOLDER/well_1_heatmap.xlsx --export-columns ${SCENARIO_PATH}/export_scenario_v1.ictemplexp --export-type xlsx --export-format heatmap --export-view well --export-filter "1 1"
+  for image in "${image_names[@]}"; do
+    ./imagec.sh --export ${MY_PATH}/test_data/test_images_v1/imagec/*/results.icdb --export-output $MY_PATH/$TARGET_FOLDER/${image}.xlsx --export-columns ${SCENARIO_PATH}/export_scenario_v1.ictemplexp --export-type xlsx --export-format list --export-view image --export-filter "1 0 $image"
+  done
+  cd ..
+  python3 convert_xlsx_to_csv.py $MY_PATH/$TARGET_FOLDER
+  cd ..
+}
+
+run_all(){
+  run_analyze_scenario_01
+  run_export_files_01
+}
+
+# Check for arguments
+if [ $# -eq 0 ]; then
+    echo "run_export script usage:"
+    echo "    [--current] Execute --execute the pipeline and store files in /tmp."
+    echo "    [--ref] Execute --execute the pipeline and store files in /ref_exports as ground truth"
+    exit 1
+fi
+
+# Parse arguments
+for arg in "$@"; do
+    case $arg in
+        --current)
+            # Execute init conan once after you initial setup the project
+            TARGET_FOLDER="tmp"
+            run_all
+            ;;
+        --ref)
+            # Execute make every time some external deps have been changed or added
+            TARGET_FOLDER="ref_exports"
+            run_all
+            ;;
+        *)
+            echo "Unknown option: $arg"
+            echo "Usage: $0 [--current] [--ref]"
+            exit 1
+            ;;
+    esac
+done
+