orGUI 1.1.0__tar.gz → 1.1.2__tar.gz

{orgui-1.1.0/orGUI.egg-info → orgui-1.1.2}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: orGUI
-Version: 1.1.0
+Version: 1.1.2
 Summary: orGUI: Orientation and Integration with 2D detectors
-Author-email: Timo Fuchs <fuchs@physik.uni-kiel.de>
+Author-email: Timo Fuchs <tfuchs@cornell.edu>
 License: MIT License
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Win32 (MS Windows)
@@ -39,6 +39,10 @@ Provides-Extra: speedup
 Requires-Dist: numba; extra == "speedup"
 Provides-Extra: extendedfilesupport
 Requires-Dist: ase; extra == "extendedfilesupport"
+Provides-Extra: full
+Requires-Dist: qtconsole; extra == "full"
+Requires-Dist: ase; extra == "full"
+Requires-Dist: numba; extra == "full"
 
 
 orGUI: Orientation and Integration with 2D detectors

{orgui-1.1.0 → orgui-1.1.2/orGUI.egg-info}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: orGUI
-Version: 1.1.0
+Version: 1.1.2
 Summary: orGUI: Orientation and Integration with 2D detectors
-Author-email: Timo Fuchs <fuchs@physik.uni-kiel.de>
+Author-email: Timo Fuchs <tfuchs@cornell.edu>
 License: MIT License
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Win32 (MS Windows)
@@ -39,6 +39,10 @@ Provides-Extra: speedup
 Requires-Dist: numba; extra == "speedup"
 Provides-Extra: extendedfilesupport
 Requires-Dist: ase; extra == "extendedfilesupport"
+Provides-Extra: full
+Requires-Dist: qtconsole; extra == "full"
+Requires-Dist: ase; extra == "full"
+Requires-Dist: numba; extra == "full"
 
 
 orGUI: Orientation and Integration with 2D detectors

{orgui-1.1.0 → orgui-1.1.2}/orGUI.egg-info/SOURCES.txt

@@ -1,8 +1,6 @@
-.gitignore
 LICENSE
 README.rst
 pyproject.toml
-requirements.txt
 orGUI.egg-info/PKG-INFO
 orGUI.egg-info/SOURCES.txt
 orGUI.egg-info/dependency_links.txt
@@ -50,8 +48,6 @@ orgui/datautils/xrayutils/test/__init__.py
 orgui/datautils/xrayutils/test/test_CTRcalc.py
 orgui/datautils/xrayutils/test/test_DetectorCalibration.py
 orgui/datautils/xrayutils/test/test_HKLcalc.py
-orgui/datautils/xrayutils/test/testdata/0V12_calculated.dat
-orgui/datautils/xrayutils/test/testdata/0V12_calculated.xpr
 orgui/datautils/xrayutils/unitcells/Fe3O4(100).bul
 orgui/datautils/xrayutils/unitcells/Pt100.bul
 orgui/datautils/xrayutils/unitcells/Pt100_small.bul
@@ -67,7 +63,12 @@ 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/diffractometer_v2.png
+orgui/resources/icons/diffractometer_v2.svg
 orgui/resources/icons/diffractometer_v3.png
+orgui/resources/icons/diffractometer_v3.svg
+orgui/resources/icons/diffractometer_v3_norm.svg
+orgui/resources/icons/diffractometer_v3_opt.svg
 orgui/resources/icons/disable-image.png
 orgui/resources/icons/disable-image.svg
 orgui/resources/icons/document-nx-open.png

{orgui-1.1.0 → orgui-1.1.2}/orGUI.egg-info/requires.txt

@@ -14,5 +14,10 @@ qtconsole
 [extendedfilesupport]
 ase
 
+[full]
+qtconsole
+ase
+numba
+
 [speedup]
 numba

{orgui-1.1.0 → orgui-1.1.2}/orgui/__init__.py

@@ -29,8 +29,8 @@ __author__ = "Timo Fuchs"
 __copyright__ = "Copyright 2020-2024 Timo Fuchs"
 __credits__ = []
 __license__ = "MIT License"
-__version__ = "1.1.0"
+__version__ = "1.1.2"
 __maintainer__ = "Timo Fuchs"
-__email__ = "fuchs@physik.uni-kiel.de"
+__email__ = "tfuchs@cornell.edu"
 
 __all__ = ['main']

{orgui-1.1.0 → orgui-1.1.2}/orgui/app/QUBCalculator.py

@@ -445,7 +445,7 @@ class QUBCalculator(qt.QSplitter):
                         ponipath = os.path.join(os.path.dirname(p), machine['poni'])
                     self.detectorCal.load(ponipath)
                     self.ubCal.setLambda(self.detectorCal.get_wavelength()*1e10)
-                    
+                    self.crystal.setEnergy(self.detectorCal.get_energy()*1e3)
                 else:
                     self.detectorCal.setFit2D(sdd*1e3,cpx,cpy,pixelX=pixelsize*1e6, pixelY=pixelsize*1e6)
                     self.detectorCal.set_wavelength(self.ubCal.getLambda()*1e-10)
@@ -468,7 +468,7 @@ class QUBCalculator(qt.QSplitter):
                     'chi' : self.chi
                 },
                 'source' :  {
-                    'E' : E
+                    'E' : self.detectorCal.get_energy()
                 },
                 'SXRD_geometry' : self.detectorCal
             }
@@ -515,7 +515,7 @@ class QUBCalculator(qt.QSplitter):
                 'chi' : self.chi
             },
             'source' :  {
-                'E' : E
+                'E' : self.detectorCal.get_energy()
             },
             'SXRD_geometry' : self.detectorCal
         }

{orgui-1.1.0 → orgui-1.1.2}/orgui/app/orGUI.py

@@ -427,7 +427,7 @@ ub : gui for UB matrix and angle calculations
                     break
                 else:
                     return
-            dist_in_pixels = min_coordinates['xy_%s' % int(which_Ewald_intersect+1)][1] - max_coordinates['xy_%s' % int(which_Ewald_intersect+1)][1]
+            dist_in_pixels = np.abs(min_coordinates['xy_%s' % int(which_Ewald_intersect+1)][1] - max_coordinates['xy_%s' % int(which_Ewald_intersect+1)][1])
             roi_hlength = np.ceil(dist_in_pixels/step_nr)
             
             # open ROI selection dialog
@@ -1020,6 +1020,13 @@ ub : gui for UB matrix and angle calculations
 
         # search files using ImportImagesScan backend
         importedscan = universalScanLoader.ImportImagesScan(filename)
+
+        if importedscan.inpath == None:
+            qt.QMessageBox.critical(self,
+                                    "Images could not be imported",
+                                    "The selected data source is not suitable\n"\
+                                    "It is necessary to select a file containing raw detector image(s)!")
+            return
         
         if importedscan.shape != self.ubcalc.detectorCal.detector.shape:
             qt.QMessageBox.critical(self,
@@ -2434,8 +2441,7 @@ class AspectRatioPixmapLabel(qt.QLabel):
 
     def sizeHint(self):
         app = qt.QApplication.instance()
-        desktopWidget = app.desktop()
-        screenGeometry = desktopWidget.screenGeometry()
+        screenGeometry = app.primaryScreen().availableGeometry()
         w = int(screenGeometry.width()/3)
         w_s = self.width()
         return qt.QSize( max(w, w_s), self.heightForWidth(w))
@@ -2452,8 +2458,8 @@ class AboutDialog(qt.QDialog):
         
         pixmap = resources.getSplashScreen(str(version))
         self.logo = qt.QLabel()
-        desktopWidget = qt.QApplication.instance().desktop()
-        screenGeometry = desktopWidget.screenGeometry()
+        app = qt.QApplication.instance()
+        screenGeometry = app.primaryScreen().availableGeometry()
         splashpm = pixmap.scaledToHeight(int(screenGeometry.height()/5), qt.Qt.SmoothTransformation)
         self.logo.setPixmap(splashpm)
         

{orgui-1.1.0 → orgui-1.1.2}/orgui/backend/backends.py

@@ -64,7 +64,7 @@ def parseID31Bliss(obj):
     return ddict
     
 # orgui will search for these counters in the Scan object and copy them into the database, if available
-auxillary_counters = ['current', 'potential', 'exposure_time', 'elapsed_time','time', 'srcur', 'mondio', 'epoch']
+auxillary_counters = ['current', 'potential', 'exposure_time', 'elapsed_time','time', 'srcur', 'mondio', 'epoch', 'potv']
     
 # assign the name parser to the beamtime identifiers:
              

{orgui-1.1.0 → orgui-1.1.2}/orgui/backend/beamline/id31_tools.py

@@ -328,6 +328,11 @@ class BlissScan_EBS(Fastscan):
                 self.th = data_1['measurement']['th_trig'][:self.nopoints] + data_1['measurement']['th_delta'][:self.nopoints] / 2
             self.axisname = 'th'
             self.mu = self.positioners['mu']
+
+        elif 'uth' in data_1['measurement']:
+            self.th = data_1['measurement']['uth'][:self.nopoints]
+            self.axisname = 'th'
+            self.mu = self.positioners['mu'] *-1
             
         elif 'mu' in data_1['measurement']:
             self.mu = data_1['measurement']['mu'][:self.nopoints]
@@ -348,6 +353,9 @@ class BlissScan_EBS(Fastscan):
             self.axisname = 'time'
             self.th = self.positioners['th']
             self.mu = self.positioners['mu']
+
+        if 'potv' in data_1['measurement']:
+            self.potv = data_1['measurement']['potv'][:self.nopoints]
             
         if 'srcur' in data_1['measurement']:
             self.srcur = data_1['measurement']['srcur'][:self.nopoints]

{orgui-1.1.0 → orgui-1.1.2}/orgui/backend/universalScanLoader.py

@@ -41,6 +41,10 @@ class ImportImagesScan():
         self.filename = imgpath
 
         self.inpath = self.find_files()
+
+        if self.inpath == None:
+            return
+
         with fabio.open(self.inpath[0] + self.inpath[1][0]) as fabf:
             img_data = fabf.data
             self.FramesPerFile = fabf.nframes
@@ -71,12 +75,14 @@ class ImportImagesScan():
         filenames = ''.join(os.listdir(selected_directory))
 
         found_scanfiles = re_str.findall(filenames) #list of found filenames (suffix only)
-        suffix = re_str.findall(self.filename)[0]
-        imagePrefix = self.filename.removesuffix(suffix)
-
         #found_scannrs = [e[1:-4] for e in found_scanfiles] #only the scan numbers, eg. 00015
-
-        return [imagePrefix,found_scanfiles]
+        if re_str.findall(self.filename) == []:
+            print('Could not load images')
+            return
+        else:
+            suffix = re_str.findall(self.filename)[0]
+            imagePrefix = self.filename.removesuffix(suffix)
+            return [imagePrefix,found_scanfiles]
 
     def set_axis(self,axismin,axismax,axis,fixedAxisValue):
         self.axis = np.linspace(axismin,axismax,self.nopoints)

{orgui-1.1.0 → orgui-1.1.2}/orgui/datautils/__init__.py

@@ -27,6 +27,6 @@ __copyright__ = "Copyright 2020-2024 Timo Fuchs"
 __license__ = "MIT License"
 __version__ = "1.0.0"
 __maintainer__ = "Timo Fuchs"
-__email__ = "fuchs@physik.uni-kiel.de"
+__email__ = "tfuchs@cornell.edu"
 
 __all__ = ['util']

{orgui-1.1.0 → orgui-1.1.2}/orgui/datautils/xrayutils/CTRcalc.py

@@ -2477,7 +2477,7 @@ class UnitCell(Lattice):
 
         for i,params in enumerate(self.basis):
             
-            radius = cov_radii_array[atomic_number(self.names[i])-1]*2
+            radius = cov_radii_array[atomic_number(self.names[i])-1][2]*2
             #elcolor_c = keyargs.get('color')
             #if elcolor_c is None:
             #    elcolor_c = elements.rgb(int(params[0]))
@@ -2496,7 +2496,7 @@ class UnitCell(Lattice):
                 for yno in range(1,abs(ucy)+1):
                     for zno in range(1,abs(ucz)+1):
                         if len(translate.shape) > 1: 
-                            x_t, y_t, z_t = np.array([x,y,z]) + translate[:,-1].A1
+                            x_t, y_t, z_t = np.array([x,y,z]) + translate[:,-1].flatten()
                             positions[no] = np.array([x_t + signx*(xno-1),y_t + signy*(yno-1),z_t + signz*(zno-1)])
                         else:
                             positions[no] = np.array([x + signx*(xno-1),y + signy*(yno-1),z+ signz*(zno-1)]) + translate
@@ -2538,7 +2538,7 @@ class UnitCell(Lattice):
                 for yno in range(1,abs(ucy)+1):
                     for zno in range(1,abs(ucz)+1):
                         if len(translate.shape) > 1: 
-                            x_t, y_t, z_t = np.array([x,y,z]) + translate[:,-1].A1
+                            x_t, y_t, z_t = np.array([x,y,z]) + translate[:,-1].flatten()
                             positions[no] = np.array([x_t + signx*(xno-1),y_t + signy*(yno-1),z_t + signz*(zno-1)])
                         else:
                             positions[no] = np.array([x + signx*(xno-1),y + signy*(yno-1),z+ signz*(zno-1)]) + translate

{orgui-1.1.0 → orgui-1.1.2}/orgui/main.py

@@ -31,7 +31,7 @@ __credits__ = []
 __license__ = "MIT License"
 from . import __version__
 __maintainer__ = "Timo Fuchs"
-__email__ = "fuchs@physik.uni-kiel.de"
+__email__ = "tfuchs@cornell.edu"
 
 import os
 import sys
@@ -76,8 +76,7 @@ def main():
         app.setWindowIcon(getQicon("orguiicon"))
         from .resources import getSplashScreen
         pixmap = getSplashScreen(__version__)
-        desktopWidget = app.desktop()
-        screenGeometry = desktopWidget.screenGeometry()
+        screenGeometry = app.primaryScreen().availableGeometry()
         splashpm = pixmap.scaledToHeight(int(screenGeometry.height()/3), qt.Qt.SmoothTransformation)
         splash = qt.QSplashScreen(splashpm)
         splash.show()

{orgui-1.1.0 → orgui-1.1.2}/orgui/resources/icons/alpha.svg

@@ -1,67 +1,67 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<svg
-   xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
-   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-   xmlns:svg="http://www.w3.org/2000/svg"
-   xmlns="http://www.w3.org/2000/svg"
-   xmlns:xlink="http://www.w3.org/1999/xlink"
-   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
-   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
-   id="svg16"
-   enable-background="new 0 0 32 32"
-   version="1.1"
-   viewBox="0 0 32 32"
-   xml:space="preserve"
-   sodipodi:docname="alpha.svg"
-   inkscape:version="0.92.3 (2405546, 2018-03-11)"
-   inkscape:export-filename="I:\icons\max_2.png"
-   inkscape:export-xdpi="96"
-   inkscape:export-ydpi="96"><defs
-   id="defs10"><linearGradient
-     inkscape:collect="always"
-     id="linearGradient825"><stop
-       style="stop-color:#000000;stop-opacity:1;"
-       offset="0"
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-       offset="1"
-       id="stop823" /></linearGradient><linearGradient
-     inkscape:collect="always"
-     xlink:href="#linearGradient825"
-     id="linearGradient827"
-     x1="3.9111714"
-     y1="15.74853"
-     x2="23.893707"
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-     gradientUnits="userSpaceOnUse" /></defs><sodipodi:namedview
-   pagecolor="#ffffff"
-   bordercolor="#666666"
-   borderopacity="1"
-   objecttolerance="10"
-   gridtolerance="10"
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-   id="rect819"
-   width="23.720406"
-   height="23.720406"
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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
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+   xmlns:xlink="http://www.w3.org/1999/xlink"
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