orGUI 1.2.0__tar.gz → 1.3.0__tar.gz

{orgui-1.2.0 → orgui-1.3.0}/PKG-INFO

@@ -1,16 +1,15 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: orGUI
-Version: 1.2.0
+Version: 1.3.0
 Summary: orGUI: Orientation and Integration with 2D detectors
 Author-email: Timo Fuchs <tfuchs@cornell.edu>
-License: MIT License
+License-Expression: MIT
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Win32 (MS Windows)
 Classifier: Environment :: X11 Applications :: Qt
 Classifier: Intended Audience :: End Users/Desktop
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
@@ -21,7 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy>=1.12
@@ -44,6 +43,7 @@ Requires-Dist: qtconsole; extra == "full"
 Requires-Dist: ase; extra == "full"
 Requires-Dist: numba; extra == "full"
 Requires-Dist: PyOpenGL; extra == "full"
+Dynamic: license-file
 
 
 orGUI: Orientation and Integration with 2D detectors

{orgui-1.2.0 → orgui-1.3.0}/orGUI.egg-info/PKG-INFO

@@ -1,16 +1,15 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: orGUI
-Version: 1.2.0
+Version: 1.3.0
 Summary: orGUI: Orientation and Integration with 2D detectors
 Author-email: Timo Fuchs <tfuchs@cornell.edu>
-License: MIT License
+License-Expression: MIT
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Win32 (MS Windows)
 Classifier: Environment :: X11 Applications :: Qt
 Classifier: Intended Audience :: End Users/Desktop
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
@@ -21,7 +20,7 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy>=1.12
@@ -44,6 +43,7 @@ Requires-Dist: qtconsole; extra == "full"
 Requires-Dist: ase; extra == "full"
 Requires-Dist: numba; extra == "full"
 Requires-Dist: PyOpenGL; extra == "full"
+Dynamic: license-file
 
 
 orGUI: Orientation and Integration with 2D detectors

{orgui-1.2.0 → orgui-1.3.0}/orGUI.egg-info/SOURCES.txt

@@ -9,21 +9,17 @@ orGUI.egg-info/requires.txt
 orGUI.egg-info/top_level.txt
 orgui/__init__.py
 orgui/main.py
-orgui.egg-info/PKG-INFO
-orgui.egg-info/SOURCES.txt
-orgui.egg-info/dependency_links.txt
-orgui.egg-info/entry_points.txt
-orgui.egg-info/requires.txt
-orgui.egg-info/top_level.txt
 orgui/app/ArrayTableDialog.py
 orgui/app/QHKLDialog.py
 orgui/app/QReflectionSelector.py
 orgui/app/QScanSelector.py
 orgui/app/QUBCalculator.py
 orgui/app/__init__.py
+orgui/app/_roi_sum_accel.py
 orgui/app/bgroi.py
 orgui/app/database.py
 orgui/app/orGUI.py
+orgui/app/peak1Dintegr.py
 orgui/app/qutils.py
 orgui/backend/__init__.py
 orgui/backend/backends.py
@@ -38,8 +34,11 @@ orgui/backend/beamline/id31_tools.py
 orgui/datautils/__init__.py
 orgui/datautils/util.py
 orgui/datautils/xrayutils/CTRcalc.py
+orgui/datautils/xrayutils/CTRfilm.py
 orgui/datautils/xrayutils/CTRopt.py
 orgui/datautils/xrayutils/CTRplotutil.py
+orgui/datautils/xrayutils/CTRuc.py
+orgui/datautils/xrayutils/CTRutil.py
 orgui/datautils/xrayutils/DetectorCalibration.py
 orgui/datautils/xrayutils/HKLVlieg.py
 orgui/datautils/xrayutils/ReciprocalNavigation.py
@@ -65,13 +64,19 @@ orgui/datautils/xrayutils/unitcells/a-PtO2(0001).bul
 orgui/resources/__init__.py
 orgui/resources/icons/alpha.png
 orgui/resources/icons/alpha.svg
+orgui/resources/icons/anchor-ROI.png
+orgui/resources/icons/anchor-ROI.svg
 orgui/resources/icons/diffractometer_v3.png
 orgui/resources/icons/disable-image.png
 orgui/resources/icons/disable-image.svg
+orgui/resources/icons/document-nx-new.png
+orgui/resources/icons/document-nx-new.svg
 orgui/resources/icons/document-nx-open.png
 orgui/resources/icons/document-nx-open.svg
 orgui/resources/icons/document-nx-save.png
 orgui/resources/icons/document-nx-save.svg
+orgui/resources/icons/incident_corrections.png
+orgui/resources/icons/incident_corrections.svg
 orgui/resources/icons/intersect_s1.png
 orgui/resources/icons/intersect_s1.svg
 orgui/resources/icons/intersect_s2.png
@@ -86,6 +91,8 @@ orgui/resources/icons/lattice-view.png
 orgui/resources/icons/lattice-view.svg
 orgui/resources/icons/logo.png
 orgui/resources/icons/logo.svg
+orgui/resources/icons/logo_v1.png
+orgui/resources/icons/logo_v1.svg
 orgui/resources/icons/max_image.png
 orgui/resources/icons/max_image.svg
 orgui/resources/icons/max_image2.png

{orgui-1.2.0 → orgui-1.3.0}/orgui/__init__.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # /*##########################################################################
 #
-# Copyright (c) 2020-2024 Timo Fuchs
+# Copyright (c) 2020-2025 Timo Fuchs
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -26,10 +26,10 @@
 
 """
 __author__ = "Timo Fuchs"
-__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__copyright__ = "Copyright 2020-2025 Timo Fuchs"
 __credits__ = []
 __license__ = "MIT License"
-__version__ = "1.2.0"
+__version__ = "1.3.0"
 __maintainer__ = "Timo Fuchs"
 __email__ = "tfuchs@cornell.edu"
 

{orgui-1.2.0 → orgui-1.3.0}/orgui/app/ArrayTableDialog.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # /*##########################################################################
 #
-# Copyright (c) 2020-2024 Timo Fuchs
+# Copyright (c) 2020-2025 Timo Fuchs
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,11 +23,11 @@
 #
 # ###########################################################################*/
 __author__ = "Timo Fuchs"
-__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__copyright__ = "Copyright 2020-2025 Timo Fuchs"
 __license__ = "MIT License"
-__version__ = "1.0.0"
+__version__ = "1.3.0"
 __maintainer__ = "Timo Fuchs"
-__email__ = "fuchs@physik.uni-kiel.de"
+__email__ = "tfuchs@cornell.edu"
 
 import numpy as np
 import os

{orgui-1.2.0 → orgui-1.3.0}/orgui/app/QHKLDialog.py

@@ -1,3 +1,34 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2025 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2025 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.3.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "tfuchs@cornell.edu"
+
 from silx.gui import qt
 from . import qutils
 import numpy as np

{orgui-1.2.0 → orgui-1.3.0}/orgui/app/QReflectionSelector.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # /*##########################################################################
 #
-# Copyright (c) 2020-2024 Timo Fuchs
+# Copyright (c) 2020-2025 Timo Fuchs
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,11 +23,11 @@
 #
 # ###########################################################################*/
 __author__ = "Timo Fuchs"
-__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__copyright__ = "Copyright 2020-2025 Timo Fuchs"
 __license__ = "MIT License"
-__version__ = "1.0.0"
+__version__ = "1.3.0"
 __maintainer__ = "Timo Fuchs"
-__email__ = "fuchs@physik.uni-kiel.de"
+__email__ = "tfuchs@cornell.edu"
 
 import sys
 import traceback
@@ -38,6 +38,7 @@ from .ArrayTableDialog import ArrayEditWidget
 from collections import OrderedDict
 from dataclasses import dataclass, field
 from typing import ClassVar
+import copy
 
 import numpy as np
 from ..datautils.xrayutils import HKLVlieg
@@ -305,7 +306,7 @@ class QReflectionSelector(qt.QSplitter):
             else:
                 self.setReflections([])
         except Exception:
-            qt.QMessageBox.critical(self,"Cannot read reflections", "Cannot read reeflections %s" % traceback.format_exc())
+            qt.QMessageBox.critical(self,"Cannot read reflections", "Cannot read reflections %s" % traceback.format_exc())
             return
             
     def clearPlotRefReflections(self):
@@ -326,7 +327,7 @@ class QReflectionSelector(qt.QSplitter):
         
             
     def redrawRefReflections(self):
-        self.setReflections(self.reflections)
+        self.setReflections(copy.deepcopy(self.reflections))
         
     def setReflections(self,refls):
         self.clearPlotRefReflections()

{orgui-1.2.0 → orgui-1.3.0}/orgui/app/QScanSelector.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # /*##########################################################################
 #
-# Copyright (c) 2020-2024 Timo Fuchs, Finn Schroeter
+# Copyright (c) 2020-2025 Timo Fuchs
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,11 +23,11 @@
 #
 # ###########################################################################*/
 __author__ = "Timo Fuchs"
-__copyright__ = "Copyright 2020-2024 Timo Fuchs, Finn Schroeter"
+__copyright__ = "Copyright 2020-2025 Timo Fuchs"
 __license__ = "MIT License"
-__version__ = "1.2.0"
+__version__ = "1.3.0"
 __maintainer__ = "Timo Fuchs"
-__email__ = "fuchs@physik.uni-kiel.de"
+__email__ = "tfuchs@cornell.edu"
 
 
 import sys
@@ -685,10 +685,42 @@ class QScanSelector(qt.QMainWindow):
                         qt.QMessageBox.Ok, self)
             clickedbutton = msgbox.exec()
             return
+        
+        # initialize dict to return scan information
         ddict = dict()
         ddict['event'] = "loadScan"
+
+        # must contain scan filepath
         ddict['file'] = self.pathedit.text()
+
+        # additional information
         ddict['scanno'] = self.scannoBox.value()
+        ddict['name'] = os.path.splitext(os.path.basename(self.pathedit.text()))[0] + '.' + str(self.scannoBox.value())
+        ddict['beamtime'] = self.btid.currentText()
+
+        # fill dict with information from active h5 node - if it matches loaded scan
+        nodes = list(self.hdfTreeView.selectedH5Nodes())
+        if not nodes == []:
+            obj = nodes[0]
+            
+            if obj.local_filename == self.pathedit.text() and obj.basename[0] == self.scannoBox.value():
+                ddict['node'] = obj
+
+                # beamtime auto detect
+                dt = dateparser.parse(obj.h5py_target['start_time'][()])
+                btid = backends.getBeamtimeId(dt)
+                ddict['beamtime'] = btid
+
+                # set detected beamtime in GUI
+                if btid in [self.btid.itemText(i) for i in range(self.btid.count())]:
+                    self.btid.setCurrentIndex(self.btid.findText(btid))
+
+                # update name to match scheme from _onNEXUSDoubleClicked function
+                ddict2 = backends.fscans[btid].parse_h5_node(obj)
+                ddict['name'] = ddict2['name']
+            else:
+                print('active node does not match selected file')
+
         self.sigScanChanged.emit(ddict)
         
     def _onLoadBackend(self):

{orgui-1.2.0 → orgui-1.3.0}/orgui/app/QUBCalculator.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 # /*##########################################################################
 #
-# Copyright (c) 2020-2024 Timo Fuchs
+# Copyright (c) 2020-2025 Timo Fuchs
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -23,11 +23,11 @@
 #
 # ###########################################################################*/
 __author__ = "Timo Fuchs"
-__copyright__ = "Copyright 2020-2024 Timo Fuchs"
+__copyright__ = "Copyright 2020-2025 Timo Fuchs"
 __license__ = "MIT License"
-__version__ = "1.0.1"
+__version__ = "1.3.0"
 __maintainer__ = "Timo Fuchs"
-__email__ = "fuchs@physik.uni-kiel.de"
+__email__ = "tfuchs@cornell.edu"
 
 from io import StringIO
 from silx.gui import qt
@@ -241,7 +241,18 @@ class QUBCalculator(qt.QSplitter):
         if self.mainGui.fscan is not None:
             if axisname is None:
                 axisname = self.mainGui.fscan.axisname
-        mu_cryst = HKLVlieg.crystalAngles_singleArray(self.mu,self.n)
+            mu, om = self.mainGui.getMuOm()
+        else:
+            mu = self.mu; om = 0.0
+        angle_factors = np.unique((om+np.pi) // (2*np.pi)) # possible angle offset factors
+        angle_factors = np.sort(angle_factors)[::-1]  # prefer solutions close to offset factor of 0, first positive elements
+        srt = np.argsort(np.abs(angle_factors))
+        angle_factors = angle_factors[srt] # prefer solutions close to offset factor of 0
+        
+        ommax = np.amax(om)
+        ommin = np.amin(om)
+        
+        mu_cryst = HKLVlieg.crystalAngles_singleArray(mu,self.n)
         hkl = np.asarray(hkl)
         if len(hkl.shape) > 1:
             hkl = hkl.T # for anglesZmode, is a bit inconsistent
@@ -253,18 +264,78 @@ class QUBCalculator(qt.QSplitter):
             pos1 = self.angles.anglesZmode(hkl,mu_cryst,'eq',self.chi,self.phi,mirrorx=False)
             pos2 = self.angles.anglesZmode(hkl,mu_cryst,'eq',self.chi,self.phi,mirrorx=True)
         else:
-            raise Exception("No scan axis given or no scan loaded.")
+            raise ValueError("No scan axis given or no scan loaded.")
 
         pos1_refr = HKLVlieg.vacAngles(pos1,self.n)
         pos2_refr = HKLVlieg.vacAngles(pos2,self.n)
         
+        def _adjust_omega_array(omega, ommin, ommax, angle_factors):
+            """ Original function, numpy parralelized with AI:
+            It finds a 'best guess' for the om range used by the experiment
+            The order of the tested angle_factors determines the priority.
+            I.e. it should usually start (highest priority) with zero and increase.
+            
+            minfactor = 0
+            metric = np.inf
+            for factor in angle_factors:
+                if ommin <= omega1 + factor*np.pi <= ommax:
+                    omega1 = omega1 + factor*np.pi
+                    break
+                else:
+                    fmetric = min( abs(omega1 + factor*np.pi  - ommin) , abs(omega1 + factor*np.pi  - ommax))
+                    if fmetric < metric:
+                        minfactor = factor
+                        metric = fmetric
+            else:
+                omega1 = omega1 + minfactor*np.pi
+            """
+            omega = np.atleast_1d(omega)
+            angle_factors = np.atleast_1d(angle_factors)
+
+            
+            # Compute all candidate shifts: shape = (N, M)
+            # N = len(omega), M = len(angle_factors)
+            candidates = omega[:, None] + angle_factors[None, :] * 2 *np.pi
+
+            # Determine which candidates lie within [ommin, ommax]
+            inside = (candidates >= ommin) & (candidates <= ommax)
+
+            # For each ω₁, find the first factor that yields an “inside” result
+            first_inside_idx = np.argmax(inside, axis=1)
+            has_inside = inside.any(axis=1)
+
+            # Compute distance to the nearest bound for all candidates
+            dist_to_min = np.abs(candidates - ommin)
+            dist_to_max = np.abs(candidates - ommax)
+            nearest_dist = np.minimum(dist_to_min, dist_to_max)
+
+            # For those with no “inside” candidate, pick the factor with minimal distance
+            closest_idx = np.argmin(nearest_dist, axis=1)
+
+            # Choose per-row index: first_inside_idx if in‐range exists, else closest_idx
+            choice_idx = np.where(has_inside, first_inside_idx, closest_idx)
+
+            # Extract the adjusted ω₁ values
+            adjusted = candidates[np.arange(omega.shape[0]), choice_idx]
+            return adjusted
+
         if len(hkl.shape) > 1:
             alpha1, delta1, gamma1, omega1, chi1, phi1 = pos1_refr.T
             alpha2, delta2, gamma2, omega2, chi2, phi2 = pos2_refr.T
             hkl = hkl.T
+            omega1 = _adjust_omega_array(omega1, ommin, ommax, angle_factors)
+            omega2 = _adjust_omega_array(omega2, ommin, ommax, angle_factors)
+            pos1_refr.T[3] = omega1
+            pos2_refr.T[3] = omega2
+            
         else:
             alpha1, delta1, gamma1, omega1, chi1, phi1 = pos1_refr
             alpha2, delta2, gamma2, omega2, chi2, phi2 = pos2_refr
+            omega1 = float(np.squeeze(_adjust_omega_array(omega1, ommin, ommax, angle_factors)))
+            omega2 = float(np.squeeze(_adjust_omega_array(omega2, ommin, ommax, angle_factors)))
+            pos1_refr[3] = omega1
+            pos2_refr[3] = omega2
+                
         
         xy1 = self.detectorCal.pixelsSurfaceAngles(gamma1,delta1,alpha1)[:,::-1]
         xy2 = self.detectorCal.pixelsSurfaceAngles(gamma2,delta2,alpha2)[:,::-1]

orgui-1.3.0/orgui/app/_roi_sum_accel.py

@@ -0,0 +1,69 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2020-2024 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2020-2025 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.3.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "tfuchs@cornell.edu"
+
+
+from numba import njit, config
+
+import numpy as np
+
+config.THREADING_LAYER = 'threadsafe'
+
+@njit('f8[:,::1](f8[:,::1], b1[:, ::1], f8[:,::1], i8[:,:, ::1], i8[:,:, ::1], i8[:,:, ::1], i8[:,:, ::1], i8[:,:, ::1], f8[:,::1])', nogil=True, cache=True)
+def processImage(image,     mask,       C_corr,    croi,      leftroi,   rightroi,  toproi,   bottomroi, all_counters):
+
+    for i in range(image.shape[0]): # this is faster than image[mask] = np.nan for some reason
+        for j in range(image.shape[1]):
+            if mask[i, j]:
+                image[i, j] = np.nan
+            else:
+                image[i, j] *= C_corr[i, j]
+    
+    invmask = np.logical_not(mask)
+    
+    for i in range(croi.shape[0]):
+        ckey = croi[i]
+        leftkey = leftroi[i]
+        rightkey = rightroi[i]
+        topkey = toproi[i]
+        bottomkey = bottomroi[i]
+        
+        # signal
+        all_counters[i,0] = np.nansum(image[ckey[1, 0]: ckey[1, 1] , ckey[0, 0]: ckey[0, 1]])
+        all_counters[i,1] = np.sum(invmask[ckey[1, 0]: ckey[1, 1], ckey[0, 0]: ckey[0, 1]])
+        
+        # background
+        all_counters[i,2] = 0.
+        all_counters[i,3] = 0.
+        for key in [leftkey, rightkey, topkey, bottomkey]:
+            all_counters[i, 2] += np.nansum(image[key[1, 0]:key[1, 1], key[0, 0]:key[0, 1]])
+            all_counters[i, 3] += np.sum(invmask[key[1, 0]:key[1, 1], key[0, 0]:key[0, 1]])
+    
+    return all_counters

{orgui-1.2.0 → orgui-1.3.0}/orgui/app/bgroi.py

@@ -1,3 +1,34 @@
+# -*- coding: utf-8 -*-
+# /*##########################################################################
+#
+# Copyright (c) 2025 Timo Fuchs
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ###########################################################################*/
+__author__ = "Timo Fuchs"
+__copyright__ = "Copyright 2025 Timo Fuchs"
+__license__ = "MIT License"
+__version__ = "1.3.0"
+__maintainer__ = "Timo Fuchs"
+__email__ = "tfuchs@cornell.edu"
+
 import logging
 import numpy