MNT: minor cleanup for adding logging

README.md

@@ -39,6 +39,8 @@ If you are new to git/github, start here: [https://confluence.slac.stanford.edu/
 
 Then read the following for an overview of the development process: [https://confluence.slac.stanford.edu/pages/viewpage.action?pageId=429562464](https://confluence.slac.stanford.edu/pages/viewpage.action?pageId=429562464)
 
+For commit messages, we can try to follow the PyDM guidelines: https://slaclab.github.io/pydm/development/development.html#commit-guidelines
+
 ### Logging
 
 Logging is added to the library code, and also to the [EventScanParallelSlice.py](https://github.com/slaclab/beamtime-calibration-suite/blob/main/suite_scripts/EventScanParallelSlice.py) and

calibrationSuite/Stats.py

@@ -37,9 +37,9 @@ def accumulate(self, x, y=0):
         d = numpy.sin((numpy.array(list(range(10)))+i)/3.14159)
         s.accumulate(d, d[7])
 
-    print(s.mean())
-    print(s.rms())
-    print(s.corr(s.mean()[7], s.rms()[7]))
-    logger.info(s.mean())
-    logger.info(s.rms())
-    logger.info(s.corr(s.mean()[7], s.rms()[7]))
+    print("mean: " + str(s.mean()))
+    print("rms: " + str(s.rms()))
+    print("s.corr(s.mean()[7], s.rms()[7]): " + str(s.corr(s.mean()[7], s.rms()[7])))
+    logger.info("mean: " + str(s.mean()))
+    logger.info("rms: " + str(s.rms()))
+    logger.info("s.corr(s.mean()[7], s.rms()[7]): " + str(s.corr(s.mean()[7], s.rms()[7])))

calibrationSuite/basicSuiteScript.py

@@ -32,11 +32,11 @@ def __init__(self, analysisType='scan'):
 
         try:
             self.location = experimentHash['location']
-        except Exception:
+        except:
             pass
         try:
             self.exp = experimentHash['exp']
-        except Exception:
+        except:
             pass
         try:
         ##if True:
@@ -46,22 +46,22 @@ def __init__(self, analysisType='scan'):
                 self.ROIs.append(np.load(f+'.npy'))
             try:  ## dumb code for compatibility or expectation
                 self.ROI = self.ROIs[0]
-            except Exception:
+            except:
                 pass
         ##if False:
-        except Exception:
+        except:
             print("had trouble finding", self.ROIfileNames)
             for currName in self.ROIfileNames:
                 logger.exception("had trouble finding" + currName)        
             self.ROI = None
             self.ROIs = None
         try:
             self.singlePixels = experimentHash['singlePixels']
-        except Exception:
+        except:
             self.singlePixels = None
         try:
             self.regionSlice = experimentHash['regionSlice']
-        except Exception:
+        except:
             self.regionSlice = None
         if self.regionSlice is not None:
             self.sliceCoordinates = [[self.regionSlice[0].start,
@@ -76,13 +76,13 @@ def __init__(self, analysisType='scan'):
             self.fluxSource = experimentHash['fluxSource']
             try:
                 self.fluxChannels = experimentHash['fluxChannels']
-            except Exception:
+            except:
                 self.fluxChannels = range(8,16) ## wave8
             try:
                 self.fluxSign = experimentHash['fluxSign']
-            except Exception:
+            except:
                 self.fluxSign = 1
-        except Exception:
+        except:
             self.fluxSource = None
 
         ## for non-120 Hz running
@@ -152,7 +152,7 @@ def __init__(self, analysisType='scan'):
             self.fluxCut = args.fluxCut
         try:
             self.runRange = eval(args.runRange) ## in case needed
-        except Exception:
+        except:
             self.runRange = None
 
         self.fivePedestalRun = args.fivePedestalRun ## in case needed
@@ -217,7 +217,7 @@ def rowCommonModeCorrection(self, frame, arbitraryCut=1000):
                     frame[r, colOffset:colOffset + self.detColsPerBank] -= rowCM
                     ##if r == 280 and rand > 0.999:
                         ##print(frame[r, colOffset:colOffset + self.detColsPerBank], np.median(frame[r, colOffset:colOffset + self.detColsPerBank]))
-                except Exception:
+                except:
                     rowCM = -666
                     print("rowCM problem")
                     logger.exception("rowCM problem")
@@ -242,7 +242,7 @@ def colCommonModeCorrection(self, frame, arbitraryCut=1000):
                     frame[rowOffset:rowOffset + self.detRowsPerBank, c] -= colCM
                     ##if r == 280 and rand > 0.999:
                         ##print(frame[r, colOffset:colOffset + self.detColsPerBank], np.median(frame[r, colOffset:colOffset + self.detColsPerBank]))
-                except Exception:
+                except:
                     colCM = -666
                     print("colCM problem")
                     logger.exception("colCM problem")

calibrationSuite/fitFunctions.py

@@ -42,7 +42,7 @@ def calculateFitR2(y, fit):
 
     try:
         r2 = 1 - (ss_res / ss_tot)
-    except Exception as e:
+    except:
         r2 = 1 ## I guess
 
     return r2

calibrationSuite/psana1Base.py

@@ -34,12 +34,12 @@ def setupPsana(self):
         self.evrs = None
         try:
             self.wave8 = Detector(self.fluxSource, self.ds.env())
-        except Exception:
+        except:
             self.wave8 = None
         self.config = None
         try:
             self.controlData = Detector('ControlData')
-        except Exception:
+        except:
             self.controlData = None
 
     def getFivePedestalRunInfo(self):
@@ -73,7 +73,7 @@ def getEvtFromRunsTooSmartForMyOwnGood(self):
             try:
                 evt = next(self.ds.events())
                 yield evt
-            except Exception:
+            except:
                 continue
 
     def getEvtFromRuns(self):
@@ -87,7 +87,7 @@ def getEvtFromRuns(self):
                 print("switching to run %d" %(self.run))
                 logger.info("switching to run %d" %(self.run))
                 self.ds = self.get_ds(self.run)
-            except Exception:
+            except:
                 print("have run out of new runs")
                 logger.exception("have run out of new runs")
                 return None
@@ -106,9 +106,9 @@ def getFlux(self, evt):
             try:
                 if f<self.fluxCut:
                     return None
-            except Exception:
+            except:
                 pass
-        except Exception:
+        except:
             return None
         return f
 
@@ -124,7 +124,7 @@ def get_evrs(self):
     def isKicked(self, evt):
         try:
             evr = evt.get(EvrData.DataV4, self.evrs[0])
-        except Exception:
+        except:
             self.get_evrs()
             evr = evt.get(EvrData.DataV4, self.evrs[0])
 
@@ -138,7 +138,7 @@ def isKicked(self, evt):
             for ec in evr.fifoEvents():
                 if ec.eventCode() == 137:
                     kicked = False
-        except Exception:
+        except:
             pass
         return kicked
 

calibrationSuite/psana2Base.py

@@ -51,7 +51,7 @@ def setupPsana(self):
         try:
             self.step_value = self.myrun.Detector('step_value')
             self.step_docstring = elf.myrun.Detector('step_docstring')
-        except Exception:
+        except:
             self.step_value = self.step_docstring = None
 
 ##        self.det = Detector('%s.0:%s.%d' %(self.location, self.detType, self.camera), self.ds.env())
@@ -71,13 +71,13 @@ def setupPsana(self):
 
         try:
             self.mfxDg1 = self.myrun.Detector('MfxDg1BmMon')
-        except Exception:
+        except:
             self.mfxDg1 = None
             print("No flux source found")## if self.verbose?
             logger.exception("No flux source found")        
         try:
             self.mfxDg2 = self.myrun.Detector('MfxDg2BmMon')
-        except Exception:
+        except:
             self.mfxDg2 = None
         ## fix hardcoding in the fullness of time
         self.detEvts = 0
@@ -86,12 +86,12 @@ def setupPsana(self):
         self.evrs = None
         try:
             self.wave8 = Detector(self.fluxSource, self.ds.env())
-        except Exception as e:
+        except:
             self.wave8 = None
         self.config = None
         try:
             self.controlData = Detector('ControlData')
-        except Exception:
+        except:
             self.controlData = None
 
 ##        if self.mfxDg1 is None:
@@ -125,7 +125,7 @@ def getNextEvtFromGen(self, gen):
         for nevt, evt in enumerate(gen):
             try:
                 self.flux = self._getFlux(evt)
-            except Exception:
+            except:
                 pass
             if self.det.raw.raw(evt) is None:
                 continue
@@ -156,7 +156,7 @@ def getEvtFromRunsTooSmartForMyOwnGood(self):
             try:
                 evt = next(self.ds.events())
                 yield evt
-            except Exception:
+            except:
                 continue
 
     def getEvtFromRuns(self):
@@ -170,7 +170,7 @@ def getEvtFromRuns(self):
                 print("switching to run %d" %(self.run))
                 logger.info("switching to run %d" %(self.run))
                 self.ds = self.get_ds(self.run)
-            except Exception as e:
+            except:
                 print("have run out of new runs")
                 logger.exception("have run out of new runs")
                 return None
@@ -184,7 +184,7 @@ def getAllFluxes(self, evt):
             return None
         try:
             return self.mfxDg1.raw.peakAmplitude(evt)
-        except Exception:
+        except:
             return None
 
     def _getFlux(self, evt):
@@ -195,13 +195,13 @@ def _getFlux(self, evt):
         try:
             f = self.mfxDg1.raw.peakAmplitude(evt)[self.fluxChannels].mean()*self.fluxSign
             ##print(f)
-        except Exception:
+        except:
             #print(e)
             return None
         try:
             if f<self.fluxCut:
                 return None
-        except Exception:
+        except:
             pass
         return f
 
@@ -245,7 +245,7 @@ def getEvt(self):
             ## dumb to do the below everywhere, should best not call this method
             ##try:
             ##    self.flux = self._getFlux(evt)
-            ##except Exception as e:
+            ##except:
             ##    pass
 
         except StopIteration: