Add image self-test; postpone GSASIIctrlGUI import until needed in CIF export; clean-up a bad open/write use

Author: briantoby

GSASII/GSASIIscriptable.py

@@ -410,7 +410,8 @@ def import_generic(filename, readerlist, fmthint=None, bank=None,
         G2fil.G2Print(f'Preparing to download {filename}')
         response = requests.get(filename)
         filename = os.path.join(download_loc,fname)
-        open(filename,'wb').write(response.content)
+        with open(filename,'wb') as fp:
+            fp.write(response.content)
         G2fil.G2Print(f'File {filename} written')
     primaryReaders, secondaryReaders = [], []
     for reader in readerlist:

GSASII/exports/G2export_CIF.py

@@ -17,7 +17,6 @@
     import wx.lib.scrolledpanel as wxscroll
     import wx.lib.resizewidget as rw
     interactive = True
-    from .. import GSASIIctrlGUI as G2G
 except ImportError:
     G2G = None
     # Avoid wx dependency for Scriptable
@@ -1381,6 +1380,7 @@ def ValidateAscii(self,checklist):
                 if msg: msg += '\n'
                 msg += lbl + " contains unicode characters: " + val
         if msg:
+            from .. import GSASIIctrlGUI as G2G
             G2G.G2MessageBox(self.G2frame,
                              'Error: CIFs can contain only ASCII characters. Please change item(s) below:\n\n'+msg,
                              'Unicode not valid for CIF')
@@ -2038,6 +2038,7 @@ def WriteDistances(phasenam):
             if 'DisAglCtls' not in generalData:
                 # should not happen, since DisAglDialog should be called
                 # for all phases before getting here
+                from .. import GSASIIctrlGUI as G2G
                 dlg = G2G.DisAglDialog(
                     self.G2frame,
                     {},
@@ -3417,6 +3418,7 @@ def WriteSingleXtalData(histlbl):
         def EditAuthor(event=None):
             'dialog to edit the CIF author info'
             'Edit the CIF author name'
+            from .. import GSASIIctrlGUI as G2G
             dlg = G2G.SingleStringDialog(self.G2frame,
                                           'Get CIF Author',
                                           'Provide CIF Author name (Last, First)',
@@ -3435,6 +3437,7 @@ def EditAuthor(event=None):
 
         def EditInstNames(event=None):
             'Provide a dialog for editing instrument names; for sequential fit, only need one name'
+            from .. import GSASIIctrlGUI as G2G
             dictlist = []
             keylist = []
             lbllist = []
@@ -3468,6 +3471,7 @@ def EditRanges(event):
             '''
             but = event.GetEventObject()
             phasedict = but.phasedict
+            from .. import GSASIIctrlGUI as G2G
             dlg = G2G.DisAglDialog(
                 self.G2frame,
                 phasedict['General']['DisAglCtls'], # edited
@@ -3489,6 +3493,7 @@ def EditCIFDefaults():
             '''Fills the CIF Defaults window with controls for editing various CIF export
             parameters (mostly related to templates).
             '''
+            from .. import GSASIIctrlGUI as G2G
             if len(self.cifdefs.GetChildren()) > 0:
                 saveSize = self.cifdefs.GetSize()
                 self.cifdefs.DestroyChildren()
@@ -3659,6 +3664,7 @@ def _ResetSelT(event):
 
         def SelectDisAglFlags(event):
             'Select Distance/Angle use flags for the selected phase'
+            from .. import GSASIIctrlGUI as G2G
             phasenam = event.GetEventObject().phase
             phasedict = self.Phases[phasenam]
             SymOpList,offsetList,symOpList,G2oprList,G2opcodes = G2spc.AllOps(phasedict['General']['SGData'])
@@ -4059,6 +4065,7 @@ def SelectDisAglFlags(event):
             #i = self.Phases[phasenam]['pId']
             phasedict = self.Phases[phasenam] # pointer to current phase info
             if 'DisAglCtls' not in phasedict['General']:
+                from .. import GSASIIctrlGUI as G2G
                 dlg = G2G.DisAglDialog(
                     self.G2frame,
                     {},
@@ -4709,6 +4716,7 @@ def __init__(self,G2frame):
         self.author = ''
 
     def mergeMag(self,G2frame,ChemPhase,MagPhase):
+        from .. import GSASIIctrlGUI as G2G
         def onChange(*args,**kwargs):
             wx.CallLater(100,showMergeMag)
         def showMergeMag():
@@ -5246,6 +5254,7 @@ class EditCIFtemplate(wx.Dialog):
       saving the CIF.
     '''
     def __init__(self,parent,cifblk,loopstructure,defaultname):
+        from .. import GSASIIctrlGUI as G2G
         OKbuttons = []
         self.cifblk = cifblk
         self.loopstructure = loopstructure
@@ -5290,6 +5299,7 @@ def Post(self):
         return (self.ShowModal() == wx.ID_OK)
     def _onSave(self,event):
         'Save CIF entries in a template file'
+        from .. import GSASIIctrlGUI as G2G
         pth = G2G.GetExportPath(self.G2frame)
         dlg = wx.FileDialog(
             self, message="Save as CIF template",
@@ -5334,6 +5344,7 @@ class EditCIFpanel(wxscroll.ScrolledPanel):
     :param (other): optional keyword parameters for wx.ScrolledPanel
     '''
     def __init__(self, parent, cifblk, loopstructure, cifdic={}, OKbuttons=[], **kw):
+        from .. import GSASIIctrlGUI as G2G
         self.parent = parent
         wxscroll.ScrolledPanel.__init__(self, parent, wx.ID_ANY, **kw)
         self.vbox = None
@@ -5492,6 +5503,7 @@ def CIFEntryWidget(self,dct,item,dataname):
         numerical values and highlights them as invalid.
         Use a selection widget when there are specific enumerated values for a string.
         '''
+        from .. import GSASIIctrlGUI as G2G
         if self.cifdic.get(dataname):
             if self.cifdic[dataname].get('_enumeration'):
                 values = ['?']+self.cifdic[dataname]['_enumeration']
@@ -5648,6 +5660,7 @@ def _onResetTemplate(event):
         self.Add(hbox)
     def _onGetTemplateFile(self,event):
         'select a template file'
+        from .. import GSASIIctrlGUI as G2G
         pth = G2G.GetImportPath(self.G2frame)
         if not pth: pth = '.'
         dlg = wx.FileDialog(

tests/test_image.py

@@ -0,0 +1,68 @@
+# perform a GSAS-II refinement using GSASIIscriptable and tutorial
+# data
+
+import os
+import sys
+import tempfile
+import numpy.testing as npt
+home = os.path.dirname(__file__)
+work = tempfile.gettempdir()
+import importlib.util
+    
+G2loc = None
+try: 
+    G2loc = importlib.util.find_spec('GSASII.GSASIIscriptable')
+except ModuleNotFoundError:
+    print('ModuleNotFound for GSASII.GSASIIscriptable')
+
+if G2loc is None: # fixup path if GSASII not installed into Python
+    print('GSAS-II not installed in Python; Hacking sys.path')
+    sys.path.append(os.path.dirname(home))
+
+import GSASII
+import GSASII.GSASIIscriptable as G2sc
+
+def test_image():
+    try:
+        import requests
+    except ModuleNotFoundError:
+        print('Module requests not installed, test_image cannot be run')
+        return
+    workloc = lambda fil: os.path.join(work,fil)
+    gpx = G2sc.G2Project(newgpx=workloc('test_image.gpx'))
+    img = 'https://advancedphotonsource.github.io/GSAS-II-tutorials/2DStrain/data/nx09_strain_011.mar2300'
+    img = gpx.add_image(img, fmthint='MAR', cacheImage=True, URL=True,
+                      download_loc=None)
+#    img = gpx.add_image(fmthint='MAR', cacheImage=True,
+#                      imagefile='/tmp/download.mar2300')
+    testdir = os.path.join(os.path.dirname(os.path.abspath( __file__ )),'testinp')
+    img[0].loadControls(os.path.join(testdir,'nx09_strain_011.imctrl'))
+    img[0].GeneratePixelMask()
+    masked = sum(img[0].data['Masks']['SpotMask']['spotMask'].flatten())
+    masked_ratio = masked/img[0].data['Masks']['SpotMask']['spotMask'].size
+    msg = 'Confirm number of masked pixels is about the same'
+    assert abs(masked_ratio - 0.02372608695652174) < 0.0001, msg #+ f" {masked_ratio}, 0.02372608695652174"
+    #breakpoint()
+    plist = img[0].Integrate()
+    i = plist[0].getdata('yobs')
+    x = plist[0].getdata('x')
+    tt1,i1 = (x[233]+x[280])/2,sum(i[233:281])
+    #print(tt1,i1)
+    msg = 'Confirm 1st peak'
+    assert abs(tt1 - 2.2695) < 0.0002, msg+' pos'
+    assert abs(i1 - 4645.6850578694975) < 0.1, msg+' intensity'
+    tt6,i6 = (x[780]+x[850])/2,sum(i[780:851])
+    #print(tt6,i6)
+    msg = 'Confirm 6th peak'
+    assert abs(tt6 - 3.9450) < 0.0002, msg+' pos'
+    assert abs(i6 - 26236.795563010724) < 0.1, msg+' intensity'
+    print('OK')
+    
+if __name__ == '__main__':
+    #import GSASII.GSASIIpath as GSASIIpath
+    #GSASIIpath.InvokeDebugOpts()
+    #import time
+    #start = time.time()
+    test_image()
+    #print('elapsed=',time.time()-start)
+    

tests/testinp/nx09_strain_011.imctrl

@@ -0,0 +1,31 @@
+type:PWDR
+color:GSPaired
+wavelength:0.12398
+calibrant:CeO2  SRM674b
+distance:1118.8555366950047
+center:[np.float64(168.59496999985376), np.float64(173.45708080489564)]
+Oblique:[0.5, False]
+tilt:1.2679918237395627
+rotation:94.80104622234859
+azmthOff:0.0
+fullIntegrate:True
+LRazimuth:[0.0, 360.0]
+setdist:100.0
+IOtth:[1.5, 9.0]
+outChannels:2500
+outAzimuths:1
+invert_x:False
+invert_y:True
+DetDepth:0.0
+calibskip:0
+pixLimit:2
+cutoff:1.0
+calibdmin:1.09
+Flat Bkg:0.0
+varyList:{'dist': True, 'det-X': True, 'det-Y': True, 'tilt': True, 'phi': True, 'dep': False, 'wave': False}
+binType:2-theta
+SampleShape:Cylinder
+PolaVal:[0.99, False]
+SampleAbs:[0.0, False]
+dark image:['', -1.0]
+background image:['', -1.0]