added JF_stack calculator

src/cristallina/analysis.py

@@ -2,6 +2,7 @@ import re
 from collections import defaultdict, deque
 from pathlib import Path
 from typing import Optional
+import logging
 
 import numpy as np
 from matplotlib import pyplot as plt
@@ -13,8 +14,11 @@ from sfdata import SFDataFiles, sfdatafile, SFScanInfo
 from joblib import Memory
 
 from . import utils
+from . import channels
 from .utils import ROI
 
+logger = logging.getLogger(__name__)
+
 def setup_cachedirs(pgroup=None, cachedir=None):
     """
     Sets the path to a persistent cache directory either from the given p-group (e.g. "p20841")
@@ -329,6 +333,51 @@ def perform_image_roi_crop(
     return np.array(rois_within_batch)
 
 
+@memory.cache()
+def calculate_JF_stacks(scan : SFScanInfo, 
+                        lower_cutoff_threshold=7.6,
+                        exclude_steps: list[int] | None = None,
+                        recompute : bool=False,
+                        detector : str = "JF16T03V02"):
+    """Calculate image stacks for JF detectors in a scan."""
+    
+    stacks = []
+    I0_norms = []
+
+    for i, step in enumerate(scan):
+        if exclude_steps is not None and i in exclude_steps:
+            logger.info(f"skipping step {i}")
+            continue
+
+        #subset = step["JF17T16V01", "JF20T01V01"]
+        JF_channels = [channels.JF, channels.JF_8M, channels.JF_I0, channels.GASMONITOR]
+        available_channels = [ch.name for ch in step.channels]
+        selected_channels = [ch for ch in JF_channels if ch in available_channels]
+
+        subset = step[*selected_channels] # only I0 for test cases
+        pids_before = len(subset.pids)
+        subset.drop_missing()
+        pids_after = len(subset.pids)
+
+        if pids_before != pids_after:
+            logger.warning(f"Step {i}: dropped {pids_before - pids_after} pulse IDs due to missing data.")
+        
+        # we only consider the JF files here
+        files = [f.fname for f in step.files if "JF" in f.fname]
+
+        stack = perform_image_stack_sum(files, channel=detector, 
+                                                    lower_cutoff_threshold=lower_cutoff_threshold)
+        stacks.append(stack)
+            
+        # TODO: define roi for I0 detector
+        stack_I0 = perform_image_roi_crop(files, channel=channels.JF_I0, lower_cutoff=2,)
+        I0_norm = np.sum(stack_I0, axis=(1, 2))
+        I0_norms.append(I0_norm)
+
+    return stacks, I0_norms
+
+
+
 @memory.cache(ignore=["batch_size"])  # we ignore batch_size for caching purposes
 def calculate_image_histograms(
     filesets,

src/cristallina/uscan.py

@@ -100,8 +100,10 @@ class UnfinishedScanInfo(SFScanInfo):
 def is_finished_scan(fname):
     """ If the scan.json file is complete, valid and the files are on the disk the scan is finished.
         This does not cover the case where a scan is interrupted and continued later. 
+
+        It also relies on the behavior of RA that the scan.json is only fully written at the end of the scan.
         
-        It also relies on the behavior of RA that the scan.json is only fully written at the end of the scan."""
+        TODO: A clear criterion for a finished scan would be that another later scan exists."""
     try:
         content = json_load(fname)
         files = [file for step in content['scan_files'] for file in step]