From bf7f62adffd3cfcba5be6844447326efcd136e47 Mon Sep 17 00:00:00 2001
From: Sven Augustin <sven.augustin@psi.ch>
Date: Fri, 2 Aug 2024 13:26:02 +0200
Subject: [PATCH] moved masking pixels out of work function

---
 dap/algos/__init__.py | 1 +
 dap/algos/mask.py     | 9 +++++++++
 dap/worker.py         | 7 ++-----
 3 files changed, 12 insertions(+), 5 deletions(-)
 create mode 100644 dap/algos/mask.py

diff --git a/dap/algos/__init__.py b/dap/algos/__init__.py
index 8b023af..e0d580e 100644
--- a/dap/algos/__init__.py
+++ b/dap/algos/__init__.py
@@ -1,5 +1,6 @@
 
 from .addmask import calc_apply_additional_mask
+from .mask import calc_mask_pixels
 from .peakfind import calc_peakfinder_analysis
 from .radprof import calc_radial_integration
 from .roi import calc_roi
diff --git a/dap/algos/mask.py b/dap/algos/mask.py
new file mode 100644
index 0000000..1ed79fa
--- /dev/null
+++ b/dap/algos/mask.py
@@ -0,0 +1,9 @@
+import numpy as np
+
+
+def calc_mask_pixels(pfdata, pixel_mask_pf):
+    if pixel_mask_pf is not None:
+        pfdata[pixel_mask_pf != 1] = np.nan #TODO: boolean mask
+
+
+
diff --git a/dap/worker.py b/dap/worker.py
index 8f7f521..3f19c4d 100644
--- a/dap/worker.py
+++ b/dap/worker.py
@@ -7,7 +7,7 @@ from time import sleep
 import jungfrau_utils as ju
 import numpy as np
 
-from algos import calc_apply_additional_mask, calc_apply_threshold, calc_peakfinder_analysis, calc_radial_integration, calc_roi, calc_spi_analysis
+from algos import calc_apply_additional_mask, calc_apply_threshold, calc_mask_pixels, calc_peakfinder_analysis, calc_radial_integration, calc_roi, calc_spi_analysis
 from utils import json_load, read_bit
 from zmqsocks import ZMQSockets
 
@@ -180,10 +180,7 @@ def work(backend_address, accumulator_host, accumulator_port, visualisation_host
     #copy image to work with peakfinder, just in case
         pfdata = np.copy(data)
 
-    # make all masked pixels values nans
-        if pixel_mask_pf is not None:
-            pfdata[pixel_mask_pf != 1] = np.nan #TODO: boolean mask
-
+        calc_mask_pixels(pfdata, pixel_mask_pf) # changes pfdata in place
         calc_apply_threshold(results, pfdata) # changes pfdata in place
         calc_roi(results, pfdata, pixel_mask_pf)
         calc_spi_analysis(results)