#@ File (label="Input folder", style="directory") inputDir #@ File (label="Output folder", style="directory") outputDir #@ File (label="Cellpose env python", style="file") envPython #@ String (label="Model", choices={"cpsam","custom"}, value="custom") modelChoice #@ File (label="Custom model (if 'custom')", style="file", required=false) customModel #@ String (label="p63+ threshold variant", choices={"T14","T1","T2","T7"}, value="T14") variant #@ String (label="Pooling mode", choices={"per_image","pool_all","pool_replicate","reference_replicate"}, value="per_image") poolingMode #@ String (label="Reference replicate (e.g. R1)", value="R1") referenceReplicate #@ Double (label="Attenuation cap", style="slider", min=0.0, max=1.0, stepSize=0.05, value=0.7) attenCap #@ Boolean (label="Use GPU", value=false) useGpu #@ Integer (label="Batch size (images per eval)", value=8) batchSize #@ Integer (label="Segmentation channel (blue)", value=3) segChannel #@ Integer (label="Quantification channel (red)", value=1) quantChannel import os import sys # Fiji does not add the script's directory to sys.path automatically; # insert it so that sidecar_runner, display, and review are importable. # # Three execution contexts require different path resolution: # 1. Plugins menu: __file__ is a relative path from the Scripts root # (e.g. "p63_quant/p63_Cellpose_Batch.py") -- resolve via IJ.getDirectory # 2. Script Editor: __file__ is not set at all -- use co_filename (always absolute) # 3. Absolute __file__: use it directly try: _script_path = __file__ except NameError: import inspect as _inspect _script_path = _inspect.currentframe().f_code.co_filename if os.path.isabs(_script_path): _here = os.path.dirname(_script_path) else: # Relative path (e.g. "p63_quant/p63_Cellpose_Batch.py" from plugins menu). # Build a prioritised list of base directories to search; the first one # that contains sidecar_runner.py wins. from ij import IJ as _IJ _rel_dir = os.path.dirname(_script_path) # e.g. "p63_quant" _p = _IJ.getDirectory("plugins") or "" _ij = _IJ.getDirectory("imagej") or "" _cwd = os.getcwd() _IJ.log("[p63] plugins={} imagej={} cwd={} rel={}".format(_p, _ij, _cwd, _rel_dir)) _search_bases = [] if _p: _search_bases.append(os.path.join(_p, "Scripts")) _search_bases.append(_p) if _ij: _search_bases.append(os.path.join(_ij, "plugins", "Scripts")) _search_bases.append(_ij) _search_bases.append(_cwd) # Jython may have the Scripts root already in sys.path for _sp in sys.path: if _sp: _search_bases.append(str(_sp)) _here = None for _base in _search_bases: _c = os.path.join(_base, _rel_dir) if os.path.isfile(os.path.join(_c, "sidecar_runner.py")): _here = _c break if _here is None: _here = os.path.dirname(os.path.abspath(_script_path)) _IJ.log("[p63] script dir resolved to: " + str(_here)) if _here not in sys.path: sys.path.insert(0, _here) # Jython's import machinery doesn't follow directory symlinks; add the # real (dereferenced) path as well so modules are importable either way. _real_here = os.path.realpath(_here) if _real_here != _here and _real_here not in sys.path: sys.path.insert(0, _real_here) # Resolve the sidecar script. Four layouts are supported: # 1. Repo / symlink layout: sidecar/ is a sibling of the src/ folder # (real path of _here has a ../sidecar/ next to it) # 2. Subdirectory layout: sidecar/ lives inside the scripts folder # (e.g. plugins/Scripts/Plugins/p63/sidecar/run_p63.py) # 3. Fiji update-site layout: sidecar lives in plugins/p63_sidecar/ # Standard script path is plugins/Scripts/Plugins// so # walking three levels up from _here reaches plugins/. # 4. Flat install: run_p63.py is copied into the same folder as the # Jython scripts. _real_here = os.path.realpath(_here) _sidecar_script = os.path.join(os.path.dirname(_real_here), "sidecar", "run_p63.py") if not os.path.isfile(_sidecar_script): # Subdirectory layout: sidecar/ inside the scripts folder _sidecar_script = os.path.join(_here, "sidecar", "run_p63.py") if not os.path.isfile(_sidecar_script): # Update-site layout: plugins/p63_sidecar/run_p63.py _plugins_root = os.path.dirname(os.path.dirname(os.path.dirname(_here))) _sidecar_script = os.path.join(_plugins_root, "p63_sidecar", "run_p63.py") if not os.path.isfile(_sidecar_script): # Flat install: sidecar lives alongside the src files _sidecar_script = os.path.join(_here, "run_p63.py") from ij import IJ import sidecar_runner import display import navigator def run(): """Validate inputs, launch the sidecar once over the whole folder, then display and review results per image.""" input_path = str(inputDir) output_path = str(outputDir) python_path = str(envPython) # --- Input validation --- if not os.path.isdir(input_path): IJ.error("p63 Batch", "Input folder not found:\n" + input_path) return if not os.path.isfile(python_path): IJ.error("p63 Batch", "Cellpose env Python not found:\n" + python_path) return if str(modelChoice) == "custom": custom_path = str(customModel) if customModel else "" if not custom_path or not os.path.isfile(custom_path): IJ.error("p63 Batch", "Custom model file not found:\n" + custom_path) return if not os.path.isdir(output_path): os.makedirs(output_path) # --- Launch sidecar (blocks until the whole batch is done) --- IJ.log("=== p63 Cellpose Batch ===") IJ.log("Input: " + input_path) IJ.log("Output: " + output_path) IJ.log("Variant: " + str(variant)) IJ.log("Pooling: " + str(poolingMode)) args = sidecar_runner.build_args( inputDir, outputDir, envPython, modelChoice, customModel, variant, attenCap, useGpu, segChannel, quantChannel, poolingMode, referenceReplicate, _sidecar_script, batchSize, ) try: sidecar_runner.run_sidecar(args) except RuntimeError as exc: IJ.error("p63 Batch - Sidecar Error", str(exc)) return # --- Read CSV outputs --- summary_rows = sidecar_runner.read_summary_csv(outputDir) cells_data = sidecar_runner.read_cells_csv(outputDir) if not summary_rows: IJ.log("[WARN] summary.csv is empty -- nothing to display.") return # Group cells by image for O(1) lookup in the loop below cells_by_image = {} for row in cells_data: cells_by_image.setdefault(row["image"], []).append(row) # Map basename -> original image path (for opening in Fiji) exts = {".tif", ".tiff", ".png", ".jpg", ".jpeg"} image_map = {} for fname in os.listdir(input_path): base, ext = os.path.splitext(fname) if ext.lower() in exts: image_map[base] = os.path.join(input_path, fname) variant_str = str(variant) threshold_col = variant_str.lower() + "_threshold" # Build a single ResultsTable for the whole batch rt = display.populate_results_table(cells_data) # --- Batch navigator: replaces the per-image sequential review loop --- navigator.show_navigator( summary_rows, cells_by_image, image_map, output_path, variant_str, threshold_col, int(segChannel), int(quantChannel), rt, ) IJ.log("=== p63 Cellpose Batch complete ===") run()