Update integration_of_tmeq_modules.py

Author: yuminguw

src/tme_quant/src/examples/integration_of_tmeq_modules.py

@@ -0,0 +1,112 @@
+"""
+Complete integration example showing all modules working together.
+"""
+
+from tme_quant.core.project import TMEProject
+from tme_quant.cell_analysis import CellAnalyzer
+from tme_quant.fiber_analysis import FiberAnalyzer
+from tme_quant.tme_analysis import TMEAnalyzer
+
+# ============================================================
+# STEP 1: Project Setup
+# ============================================================
+
+project = TMEProject(name="Complete_TME_Analysis")
+
+project.add_image(
+    image_id="sample_001",
+    channels={'nuclei': 0, 'collagen': 1},
+    pixel_size=(0.5, 0.5)
+)
+
+# ============================================================
+# STEP 2: Cell Analysis (Using cell_analysis module)
+# ============================================================
+
+cell_analyzer = CellAnalyzer()
+
+# Segment
+seg_result = cell_analyzer.segment_cells_2d(
+    cell_image, seg_params
+)
+
+# Classify
+class_result = cell_analyzer.classify_cells(
+    seg_result, class_params, image
+)
+
+# Quantify
+quant_result = cell_analyzer.quantify_cells(
+    seg_result, quant_params, image
+)
+
+# Add to project
+for cell_props in seg_result.cells:
+    cell_obj = create_cell_object_from_segmentation(
+        cell_props, parent_id="sample_001"
+    )
+    # Add classification
+    cell_id = cell_props.cell_id
+    if cell_id in class_result.cell_types:
+        cell_obj.cell_type = class_result.cell_types[cell_id]
+    
+    project.add_object(cell_obj)
+
+# ============================================================
+# STEP 3: Fiber Analysis (Using fiber_analysis module)
+# ============================================================
+
+fiber_analyzer = FiberAnalyzer()
+
+# Extract
+fiber_result = fiber_analyzer.extract_fibers_2d(
+    fiber_image, extract_params
+)
+
+# Add to project
+for fiber_props in fiber_result.fibers:
+    fiber_obj = create_fiber_object_from_extraction(
+        fiber_props, parent_id="sample_001"
+    )
+    project.add_object(fiber_obj)
+
+# ============================================================
+# STEP 4: TME Analysis (Using NEW tme_analysis module)
+# ============================================================
+
+tme_analyzer = TMEAnalyzer()
+
+# Detect tumor regions
+tumor_regions = tme_analyzer.detect_tumor_regions(
+    project.get_objects_by_type("cell"),
+    tumor_params
+)
+
+for tumor in tumor_regions:
+    project.add_object(tumor)
+
+# Run TACS analysis
+tacs_result = tme_analyzer.analyze(
+    cells=project.get_objects_by_type("cell"),
+    fibers=project.get_objects_by_type("fiber"),
+    tumor_regions=tumor_regions,
+    params=tacs_params
+)
+
+# ============================================================
+# STEP 5: Export Everything
+# ============================================================
+
+# Export project
+project.save("output/project.tme")
+
+# Export cell analysis
+cell_analyzer.export_results("output/cells/")
+
+# Export fiber analysis
+fiber_analyzer.export_results("output/fibers/")
+
+# Export TME analysis
+tme_analyzer.export_results("output/tme/")
+
+print("Complete TME analysis pipeline finished!")