From 6758f3cc6d8e7914c6f7c5e5bc3dae10fda66551 Mon Sep 17 00:00:00 2001
From: Alexander Steppke <alexander.steppke@psi.ch>
Date: Sat, 18 Jan 2025 20:26:35 +0100
Subject: [PATCH] Thresholding and sum part 2

---
 src/cristallina/analysis.py | 8 +++++++-
 src/cristallina/channels.py | 6 ++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/cristallina/analysis.py b/src/cristallina/analysis.py
index 3219940..3a773b8 100644
--- a/src/cristallina/analysis.py
+++ b/src/cristallina/analysis.py
@@ -10,7 +10,6 @@ import lmfit
 
 from sfdata import SFDataFiles, sfdatafile, SFScanInfo
 
-import joblib
 from joblib import Memory
 
 from . import utils
@@ -68,6 +67,7 @@ def perform_image_calculations(
     roi: Optional[ROI] = None,
     preview=False,
     operations=["sum"],
+    lower_cutoff_threshold=None,
 ):
     """
     Performs one or more calculations ("sum", "mean" or "std") for a given region of interest (roi)
@@ -112,6 +112,10 @@ def perform_image_calculations(
             else:
                 im_ROI = im[:, roi.rows, roi.cols]
 
+            # use cutoff to set values to 0 below
+            if lower_cutoff_threshold is not None:
+                im_ROI = np.where(im_ROI < lower_cutoff_threshold, 0, im_ROI)
+
             # iterate over all operations
             for op in operations:
                 label, func = possible_operations[op]
@@ -134,6 +138,7 @@ def sum_images(
     batch_size=10,
     roi: Optional[ROI] = None,
     preview=False,
+    lower_cutoff_threshold=None,
 ):
     """
     Sums a given region of interest (roi) for an image channel from a
@@ -157,6 +162,7 @@ def sum_images(
         roi=roi,
         preview=preview,
         operations=["sum"],
+        lower_cutoff_threshold=lower_cutoff_threshold,
     )
 
 
diff --git a/src/cristallina/channels.py b/src/cristallina/channels.py
index 413cd1e..01ce4fb 100644
--- a/src/cristallina/channels.py
+++ b/src/cristallina/channels.py
@@ -11,6 +11,10 @@ JF = 'JF16T03V01'
 # Jungfrau 8M detector
 JF_8M = "JF17T16V01"
 
+# JF I0 monitor and stripcell detector
+JF_I0 = 'JF20T01V01'
+JF_strip = 'JF05T01V01'
+
 # PSSS
 PSSS_X = 'SARFE10-PSSS059:SPECTRUM_X'
 PSSS_Y = 'SARFE10-PSSS059:SPECTRUM_Y'
@@ -24,3 +28,5 @@ PBPS053_intensity = "SARFE10-PBPS053:INTENSITY"
 
 # X-ray eye
 XEYE = "SARES30-CAMS156-XE:FPICTURE"
+
+