Bug fixes for RHEL9

CrystalPlan_version.py

@@ -16,7 +16,7 @@
 #            revision = re.match("Revision: (\d+)", line).group(1)
 #    return revision
 
-version = '1.5'
+version = '1.6'
 package_name = 'CrystalPlan'
 description = \
 """CrystalPlan is an experiment planning tool for crystallography. You can choose an instrument and supply your sample's lattice parameters to simulate which reflections will be measured, by which detectors and at what wavelengths."""

crystalplan.py

@@ -33,4 +33,4 @@
 
 import CrystalPlan.gui.main
 if __name__ == '__main__':
-    CrystalPlan.gui.main.handle_arguments_and_launch(InstalledVersion=True)
+    CrystalPlan.gui.main.handle_arguments_and_launch(InstalledVersion=False)

crystalplan.yml

@@ -0,0 +1,26 @@
+---
+
+name: crystalplan
+
+channels:
+  - free
+  - conda-forge
+
+dependencies:
+  - python=2.7
+  - traitsui=5.0.0
+  - mayavi=4.5.0
+  - apptools=4.4.0
+  - jsoncpp=0.10.6
+  - wxpython=3.0.0
+  - numpy
+  - matplotlib
+  - vtk=7.1.0
+  - weave
+  - scipy
+  - gdk-pixbuf
+  - atk
+  - gxx_linux-64
+  - pip
+
+

gui/dialog_edit_crystal.py

@@ -270,7 +270,7 @@ def OnButtonGenerateUB(self, event):
     def OnButtonReadUB(self, event):
         """Ask the user to find the UB matrix file"""
         filename = self.crystal.ub_matrix_last_filename
-        (path, ignored) = os.path.split( os.path.abspath(filename) )
+        (path, filename) = os.path.split( os.path.abspath(filename) )
         filters = 'All files (*)|*|Text files (*.txt)|*.txt'
         dialog = wx.FileDialog ( self, defaultFile=filename, defaultDir=path, message='Choose a UB matrix file', wildcard=filters, style=wx.OPEN )
         if dialog.ShowModal() == wx.ID_OK:

gui/panel_reflection_measurement.py

@@ -233,17 +233,22 @@ def set_measurement(self, refl, meas):
 
             #Remove these windows, if they are in there
             try:
-                self.flexGridSizer1.RemoveWindow(self.staticTextIntegrated)
-                self.flexGridSizer1.RemoveWindow(self.buttonPlace)
+                self.flexGridSizer1.Remove(self.staticTextIntegrated)
             except:
                 pass
-
+            try:
+                self.flexGridSizer1.Remove(self.buttonPlace)
+            except:
+                pass
+
             if hasattr(meas, "integrated"):
                 #Real measurement
                 self.staticTextWidthLabel.SetLabel(" SigI:")
                 self.staticTextWidth.SetLabel((self.fmt_counts % meas.sigI))
                 self.staticTextWidth.SetToolTipString(u'Sigma I of the integrated peak intensity')
                 self.staticTextIntegrated.SetLabel((self.fmt_counts % meas.integrated))
+                self.flexGridSizer1.Detach(self.buttonPlace)
+                self.flexGridSizer1.Detach(self.staticTextIntegrated)
                 self.flexGridSizer1.InsertWindow(9, self.staticTextIntegrated, 0, border=0, flag=wx.SHRINK)
                 self.staticTextIntegratedLabel.Show()
                 self.staticTextIntegrated.Show()
@@ -253,6 +258,8 @@ def set_measurement(self, refl, meas):
                 self.staticTextWidthLabel.SetLabel("Width:")
                 self.staticTextWidth.SetLabel((fmt % meas.peak_width) + " mm")
                 self.staticTextWidth.SetToolTipString(u'Half-width of the peak on the detector.')
+                self.flexGridSizer1.Detach(self.buttonPlace)
+                self.flexGridSizer1.Detach(self.staticTextIntegrated)
                 self.flexGridSizer1.InsertWindow(9, self.buttonPlace, 0, border=8, flag=wx.EXPAND | wx.RIGHT)
                 # Don't show the place button for 4-circle
                 self.buttonPlace.Show( not gui_utils.fourcircle_mode() )

model/crystal_calc.py

@@ -378,7 +378,6 @@ def getq_python(azimuth, elevation, wl_output, rot_matrix, wl_input=None):
 {
     py::tuple return_val(3);
     double wl_input = wl_output;
-    
 """
 
 
@@ -418,7 +417,7 @@ def getq_python(azimuth, elevation, wl_output, rot_matrix, wl_input=None):
     q[1]=qx * rot_matrix[3+0] + qy * rot_matrix[3+1] + qz * rot_matrix[3+2];
     q[2]=qx * rot_matrix[6+0] + qy * rot_matrix[6+1] + qz * rot_matrix[6+2];
     return_val = q;
-    """
+"""
 getq_code_footer = "return return_val; }"
 
 

model/detectors.py

@@ -413,8 +413,7 @@ def get_detector_coordinates(self, beam, wl_min=0.0, wl_max=1e6):
                 hits_it[i] = (v > -height/2) && (v < height/2) && (h > -width/2) && (h < width/2);
             }
         }
-        return_val = error_count;
-        """
+        return_val = error_count;"""
 
         #Generate a list of the variables used
         varlist = ['base_point', 'horizontal', 'vertical', 'normal']

model/experiment.py

@@ -1700,8 +1700,7 @@ def initialize_volume_symmetry_map(self):
                         
                     }
                 }
-            }
-            """
+            }"""
             qres = inst.q_resolution
             n = len(self.inst.qx_list)
             table = np.array(pg.table) #Turn the list of 3x3 arrays into a Nx3x3 array
@@ -1778,8 +1777,7 @@ def apply_volume_symmetry(self, use_inline_c=True):
                         //printf("%d\\n", index);
                     }
                 }
-            }
-            """
+            }"""
             varlist = ['old_q', 'qspace_flat', 'numpix', 'order', 'symm']
             weave.inline(code, varlist, compiler='gcc', support_code=support)
             #Reshape it back as a 3D array.
@@ -2032,8 +2030,7 @@ def calculate_coverage_stats(self):
             results[0] = overall_points;
             results[1] = overall_covered_points;
             results[2] = overall_redundant_points;
-            return_val = results;
-            """
+            return_val = results;"""
             ret_val = weave.inline(code,['qspace', 'qspace_radius', 'q_step', 'qlim', 'total_points', 'qspace_size', 'num', 'covered_points0', 'covered_points1', 'covered_points2', 'covered_points3'],
                                 compiler='gcc', support_code = support)
             #The function returns a tuple

model/goniometer.py

@@ -524,7 +524,7 @@ def csv_add_position(self, fileobj, angle_values, count_for, count_value, commen
         if not allowed:
             #Can't reach this position
             fileobj.write("#"" ----- ERROR! This sample orientation could not be achieved with the goniometer, because of '%s'. THE FOLLOWING LINE HAS BEEN COMMENTED OUT ------ ""\n" % reason )
-            fileobj.write('#' + csv_line( comment, das_angles + [stopping_criterion, count_value] ) )
+            fileobj.write('#' + csv_line( [comment]+ das_angles + [stopping_criterion, count_value] ) )
         else:
             #They are okay
             fileobj.write(csv_line( [comment] + das_angles + [stopping_criterion, count_value] ) )
@@ -626,8 +626,7 @@ def get_fitness_function_c_code(self):
             // if (omega < omega_min || omega > omega_max) fitness += 10;
 
             return fitness;
-        }
-        """ % (args)
+        }""" % (args)
         return s
 
 
@@ -860,8 +859,7 @@ def _angle_fitness_brute(self, rot_angle_list, initial_rotation_matrix, ending_v
             phi_list.append(phi);
             chi_list.append(chi);
             omega_list.append(omega);
-        }
-        """
+        }"""
         #Workaround for bug in weave, where it ignores any changes in the support code.
         code += "\n\n // " + self.__class__.__name__ + "\n"
         code += "/* " + self.get_fitness_function_c_code() + " */"
@@ -1095,8 +1093,7 @@ def get_fitness_function_c_code(self):
             if (phi > phi_max) fitness += (phi - phi_max) * 1.0;
 
             return fitness;
-        }
-        """ % (args)
+        }""" % (args)
         return s
 
     #-------------------------------------------------------------------------------
@@ -1236,8 +1233,7 @@ def get_fitness_function_c_code(self):
             if (phi > phi_max) fitness += (phi - phi_max) * 1.0;
 
             return fitness;
-        }
-        """ % (args)
+        }""" % (args)
         return s
 
 
@@ -1512,8 +1508,7 @@ def get_fitness_function_c_code(self):
             if (omega > omega_max) fitness += (omega - omega_max) * 1.0;
 
             return fitness;
-        }
-        """ % (args)
+        }""" % (args)
         return s
 
 
@@ -1791,8 +1786,7 @@ def get_fitness_function_c_code(self):
             // if (omega < omega_min || omega > omega_max) fitness += 10;
 
             return fitness;
-        }
-        """ % (args)
+        }""" % (args)
         return s
 
     #-------------------------------------------------------------------------------
@@ -1977,8 +1971,7 @@ def get_fitness_function_c_code(self):
             if (omega > omega_max) fitness += (omega - omega_max) * 1.0;
 
             return fitness;
-        }
-        """ % (args)
+        } """ % (args)
         return s
 
 
@@ -2849,8 +2842,7 @@ def get_fitness_function_c_code(self):
             
             return absolute(chi) + omegadiff + absolute(phi)/1000.0;
             //return absolute(chi) + omegadiff + absolute(phi);
-        }
-        """
+        }"""
 
 
     #-------------------------------------------------------------------------
@@ -2944,8 +2936,7 @@ def get_fitness_function_c_code(self):
             if (omega > omega_max) fitness += (omega - omega_max) * 1.0;
 
             return fitness;
-        }
-        """ % (args)
+        }""" % (args)
         return s
 
 

model/instrument.py

@@ -662,8 +662,7 @@ def make_qspace(self):
                         }
                     }
                 //return q_out;
-            }
-            """
+            }"""
 
     _code_calculate_coverage = """
             //Loop through pixels using the list given before.
@@ -759,8 +758,7 @@ def make_qspace(self):
 
                 } //for iiy
 
-            }
-            """
+            }"""
 
 
     #========================================================================================================
@@ -1155,10 +1153,7 @@ def total_coverage(self, detectors_used, orientations_used, use_inline_c=True):
                         }// for iy
                     }
                 } //for ix
-
-
-            }
-            """
+            }"""
             varlist = ['number_of_ints', 'coverage', 'coverage_size', 'mask1', 'mask2', 'num_coverage', 'coverage_list']
             weave.inline(code, varlist, compiler='gcc', support_code = support)
 
@@ -1339,8 +1334,7 @@ def __init__ (self, filename=None, params=dict()):
                     } //numfrac > 0 so we can draw the line
 
                 } //for iiy
-            }
-            """
+            }"""
 
     #========================================================================================================
     def calculate_coverage(self, det_list, angles, sample_U_matrix=np.identity(3), use_inline_c=True):
@@ -1632,8 +1626,7 @@ def total_coverage(self, detectors_used, orientations_used, use_inline_c=True, s
                 } //for ix
 
 
-            }
-            """
+            }"""
             varlist = ['number_of_ints', 'coverage', 'coverage_size', 'num_coverage', 'coverage_list']
             weave.inline(code, varlist, compiler='gcc', support_code = support)