Merge pull request #132 from slaclab/apply_formatting

MNT: apply 'lint_and_format.sh' script and fix some issues manually

calibrationSuite/argumentParser.py

@@ -31,8 +31,10 @@ def __init__(self):
         self.parser.add_argument("-p", "--path", type=str, help="the base path to the output directory")
         self.parser.add_argument("-n", "--nModules", type=int, help="nModules")
         self.parser.add_argument("--analyzedModules", type=str, help="of the form '[0,2,5]'")
-        self.parser.add_argument("--regionSlice", type=str, help="of the form '[0,8,0,704,0,768]' - six ints for 3d detectors")
-
+        self.parser.add_argument(
+            "--regionSlice", type=str, help="of the form '[0,8,0,704,0,768]' - six ints for 3d detectors"
+        )
+
         self.parser.add_argument(
             "--mode", type=str, help="detector mode (1d, 2d, ...?"
         )  ## might be discoverable otherwise

calibrationSuite/basicSuiteScript.py

@@ -95,17 +95,17 @@ def getRawData(self, evt, gainBitsMasked=True, negativeGain=False):
         frames = self.plainGetRawData(evt)
         if frames is None:
             return None
-        
+
         nZero = frames.size - np.count_nonzero(frames)
         try:
             dz = self.nZero - nZero
             if dz != 0:
-                print("found %d new zero pixels, expected %d, setting frame to None" %(dz, self.nZero))
+                print("found %d new zero pixels, expected %d, setting frame to None" % (dz, self.nZero))
                 return None
-        except:
+        except Exception:
             self.nZero = nZero
-            print("Starting with %d zero pixels, will require exactly that many for this run" %(nZero))
-            
+            print("Starting with %d zero pixels, will require exactly that many for this run" % (nZero))
+
         if False and self.special:  ## turned off for a tiny bit of speed
             if "thirteenBits" in self.special:
                 frames = frames & 0xFFFE

calibrationSuite/detectorInfo.py

@@ -39,17 +39,25 @@ def __init__(self, detType, detSubtype="1d", detVersion=0):
         self.cameraType = None
         self.dimension = 3  ## suite attempts not to know
         self.autoRanging = True
-
-        knownTypes = ["epixhr", "epixm", "epix100", "Epix100a",
-                      "jungfrau", "Jungfrau",## cxic00121 has no alias in run 88
-                      "epix10k", "Epix10ka", "archon"]
+
+        knownTypes = [
+            "epixhr",
+            "epixm",
+            "epix100",
+            "Epix100a",
+            "jungfrau",
+            "Jungfrau",  ## cxic00121 has no alias in run 88
+            "epix10k",
+            "Epix10ka",
+            "archon",
+        ]
         if detType not in knownTypes:
             raise Exception("type %s not in known types %s" % (detType, str(knownTypes)))
 
         self.epix10kCameraTypes = {1: "Epix10ka", 4: "Epix10kaQuad", 16: "Epix10ka2M"}
         self.jungfrauCameraTypes = {1: "Jungfrau0.5", 2: "Jungfrau1M", 8: "Jungfrau4M"}
 
-    def setupDetector(self): ## needs nModules to be set
+    def setupDetector(self):  ## needs nModules to be set
         if self.detectorType == "epixhr":
             self.setup_epixhr()
         elif self.detectorType == "epixm":
@@ -58,11 +66,11 @@ def setupDetector(self): ## needs nModules to be set
             self.setup_epix100()
         elif self.detectorType == "archon":
             self.setup_rixsCCD()
-        elif 'jungfrau' in self.detectorType.lower():
+        elif "jungfrau" in self.detectorType.lower():
             self.setup_jungfrau()
-        elif 'epix10k' in self.detectorType.lower():
+        elif "epix10k" in self.detectorType.lower():
             self.setup_epix10k()
-            
+
     def setNModules(self, n):
         self.nModules = n
 
@@ -99,9 +107,9 @@ def setup_epixM(self):
         self.preferredCommonMode = "rowCommonMode"  ## guess
         self.clusterShape = [3, 3]
         self.gainMode = None  ## may want to know about default, softHigh, softLow
-        if self.detectorVersion<1:
+        if self.detectorVersion < 1:
             self.negativeGain = True
-            print("N.b: using negative gain for version %d" %(self.detectorVersion))
+            print("N.b: using negative gain for version %d" % (self.detectorVersion))
         self.aduPerKeV = 666
         self.seedCut = 2
         self.neighborCut = 0.25  ## ditto
@@ -121,10 +129,10 @@ def setup_epix100(self):
         # need to still implement getGainMode()
         # self.gainMode = self.getGainMode()
         self.preferredCommonMode = "regionCommonMode"
-        self.aduPerKeV = 18. ## approximate
+        self.aduPerKeV = 18.0  ## approximate
         self.clusterShape = [3, 3]
         self.seedCut = 3
-        self.neighborCut = 0.5  
+        self.neighborCut = 0.5
 
     def setup_jungfrau(self):
         self.cameraType = self.jungfrauCameraTypes[self.nModules]
@@ -141,9 +149,9 @@ def setup_jungfrau(self):
         # self.gainMode = self.getGainMode()
         self.preferredCommonMode = "regionCommonMode"
         self.clusterShape = [3, 3]
-        self.aduPerKeV = 41 ## g0 only of course...
+        self.aduPerKeV = 41  ## g0 only of course...
         self.seedCut = 3
-        self.neighborCut = 0.5  
+        self.neighborCut = 0.5
 
     def setup_epix10k(self):
         self.cameraType = self.epix10kCameraTypes[self.nModules]
@@ -158,13 +166,13 @@ def setup_epix10k(self):
         # self.gainMode = self.getGainMode()
         self.preferredCommonMode = "colCommonMode"
         self.clusterShape = [3, 3]
-        self.aduPerKeV = 16 ## high gain; 5.5 for medium
+        self.aduPerKeV = 16  ## high gain; 5.5 for medium
         self.seedCut = 3
-        self.neighborCut = 0.5  
+        self.neighborCut = 0.5
 
     def setup_rixsCCD(self):
         print("rixsCCD mode:", self.detectorSubtype)
-        self.cameraType = "rixsCCD" ##+ mode ## psana should support mode
+        self.cameraType = "rixsCCD"  ##+ mode ## psana should support mode
         self.autoRanging = False
         self.nTestPixelsPerBank = 36
         self.nBanks = 16
@@ -178,5 +186,3 @@ def setup_rixsCCD(self):
             self.nRows = 1200
             self.clusterShape = [3, 5]  ## maybe
         self.g0cut = 1 << 16
-
-

calibrationSuite/fitFunctions.py

@@ -16,7 +16,8 @@
 
 logger = logging.getLogger(__name__)
 
-sqrt2pi = np.sqrt(2*np.pi)
+sqrt2pi = np.sqrt(2 * np.pi)
+
 
 def linear(x, a, b):
     return a * x + b

calibrationSuite/psana1Base.py

@@ -44,10 +44,12 @@ def setupPsana(self):
             self.run = self.runRange[0]
             self.ds = self.get_ds()
 
-##        self.det = psana.Detector("%s.0:%s.%d" % (self.location, self.detType, self.camera), self.ds.env())
-        self.det = psana.Detector("%s.0:%s.%d" % (self.location, self.detectorInfo.cameraType, self.camera), self.ds.env())
+        ##        self.det = psana.Detector("%s.0:%s.%d" % (self.location, self.detType, self.camera), self.ds.env())
+        self.det = psana.Detector(
+            "%s.0:%s.%d" % (self.location, self.detectorInfo.cameraType, self.camera), self.ds.env()
+        )
         ## this is to distinguish between epix10ka form factors, etc.
-        
+
         self.evrs = None
         try:
             self.wave8 = psana.Detector(self.fluxSource, self.ds.env())
@@ -65,13 +67,13 @@ def get_ds(self, run=None):
         ##return psana.DataSource("exp=%s:run=%d:smd" % (self.exp, run))
         return psana.MPIDataSource("exp=%s:run=%d:smd" % (self.exp, run))
 
-    def get_smalldata(self, **kwargs):##, gather_interval=100):
+    def get_smalldata(self, **kwargs):  ##, gather_interval=100):
         try:
-            return self.ds.small_data(filename=filename, gather_interval=gather_interval)
-        except:
+            return self.ds.small_data(filename=filename, gather_interval=gather_interval)  # noqa: F821
+        except Exception:
             print("can't make smalldata - is datasource defined?")
         return None
-        
+
     def getEvt(self, run=None):
         oldDs = self.ds
         if run is not None:
@@ -87,7 +89,7 @@ def getEvt(self, run=None):
     def getEventCodes(self, evt):
         ## do something smarter if ever needed
         return []
-    
+
     def getFlux(self, evt):
         try:
             fluxes = self.wave8.get(evt).peakA()

calibrationSuite/psana2Base.py

@@ -115,10 +115,10 @@ def get_ds(self, run=None):
         )  ##, dir=tmpDir)
         return ds
 
-    def get_smalldata(self, filename):##, gather_interval=100):
+    def get_smalldata(self, filename):  ##, gather_interval=100):
         try:
-            return self.ds.smalldata(filename=filename)##, gather_interval=gather_interval)
-        except:
+            return self.ds.smalldata(filename=filename)  ##, gather_interval=gather_interval)
+        except Exception:
             print("can't make smalldata - is datasource defined?")
         return None
 
@@ -255,14 +255,14 @@ def getTimestamp(self, evt):
         return evt.timestamp
 
     def getUniqueid(self):
-        return getattr(self.det, 'raw')._uniqueid
+        return getattr(self.det, "raw")._uniqueid
 
     def getPedestal(self, evt, gainMode):
         ## assumes a dimension for gainmode
         if self.detectorInfo.autoRanging:
             return self.det.calibconst["pedestals"][0][gainMode]
         return self.det.calibconst["pedestals"][0]
-            
+
     def getPingPongParity(self, frameRegion):
         evensEvenRowsOddsOddRows = frameRegion[::2, ::2] + frameRegion[1::2, 1::2]
         oddsEvenRowsEvensOddRows = frameRegion[1::2, ::2] + frameRegion[::2, 1::2]

calibrationSuite/psanaCommon.py

@@ -32,8 +32,8 @@ def __init__(self, analysisType="scan"):
         print("in psanaCommon")
         logger.info("in psanaCommon")
 
-        self.analysisType = analysisType ## fix below
-        
+        self.analysisType = analysisType  ## fix below
+
         self.args = ArgumentParser().parse_args()
         logger.info("parsed cmdline args: " + str(self.args))
 
@@ -59,6 +59,7 @@ def __init__(self, analysisType="scan"):
         self.setupFromHashOrCmd()
         self.setupOutputDirString(analysisType)
         self.setupConfigHash()
+
     #### Start of setup related functions ####
 
     def loadExperimentHashFromConfig(self):
@@ -113,28 +114,24 @@ def setupFromExperimentHash(self):
 
         try:
             detVersion = self.experimentHash["detectorVersion"]
-        except:
+        except Exception:
             detVersion = 0
 
         try:
             self.detectorInfo = DetectorInfo(
                 self.experimentHash["detectorType"],
                 detSubtype=self.experimentHash["detectorSubtype"],
-                detVersion=detVersion
+                detVersion=detVersion,
             )
         except Exception:
-            self.detectorInfo = DetectorInfo(
-                self.experimentHash["detectorType"],
-                detVersion=detVersion
-            )
+            self.detectorInfo = DetectorInfo(self.experimentHash["detectorType"], detVersion=detVersion)
 
         self.exp = self.experimentHash.get("exp", None)
 
         self.setupROIFiles()
 
         self.singlePixels = self.experimentHash.get("singlePixels", None)
 
-
         self.regionSlice = self.experimentHash.get("regionSlice", None)
         ## some code moved to setupFromHashOrCmd
         self.analyzedModules = self.experimentHash.get("analyzedModules", None)
@@ -257,20 +254,28 @@ def setupFromCmdlineArgs(self):
         else:
             self.detType = self.args.detType
             jungfrau = epix10k = False
-            if 'epix10k' in self.detType.lower():
+            if "epix10k" in self.detType.lower():
                 epix10k = True
-            elif 'jungfrau' in self.detType.lower():
+            elif "jungfrau" in self.detType.lower():
                 jungfrau = True
             ## could allow just epix10k or jungfrau + n modules...
             if epix10k or jungfrau:
                 if self.args.nModules is not None:
                     raise RuntimeError("should not specify exact detector type and n modules")
                 if epix10k:
-                    nModules = [k for k in self.detectorInfo.epix10kCameraTypes.keys() if self.detectorInfo.epix10kCameraTypes[k]==self.detType]
+                    nModules = [
+                        k
+                        for k in self.detectorInfo.epix10kCameraTypes.keys()
+                        if self.detectorInfo.epix10kCameraTypes[k] == self.detType
+                    ]
                 if jungfrau:
-                    nModules = [k for k in self.detectorInfo.jungfrauCameraTypes.keys() if self.detectorInfo.jungfrauCameraTypes[k]==self.detType]
+                    nModules = [
+                        k
+                        for k in self.detectorInfo.jungfrauCameraTypes.keys()
+                        if self.detectorInfo.jungfrauCameraTypes[k] == self.detType
+                    ]
                 if nModules == []:
-                    raise RuntimeError("could not determine n modules from detector type %s" %(self.detType))
+                    raise RuntimeError("could not determine n modules from detector type %s" % (self.detType))
                 self.detectorInfo.setNModules(nModules[0])
 
         self.detectorInfo.setupDetector()
@@ -287,7 +292,7 @@ def setupFromCmdlineArgs(self):
             regionSliceArray = eval(self.args.regionSlice)
             if len(regionSliceArray) != 6:
                 raise RuntimeError("expect 6 elements in region slice")
-            a,b,c,d,e,f = regionSliceArray
+            a, b, c, d, e, f = regionSliceArray
             self.regionSlice = np.s_[a:b, c:d, e:f]
 
         self.g0cut = self.detectorInfo.g0cut
@@ -344,15 +349,15 @@ def setupFromHashOrCmd(self):
         if self.regionSlice is not None:
             ## n.b. expects 3d slice definition regardless for consistency
             if self.detectorInfo.dimension == 3:
-                offset = 1
+                self.offset = 1
             self.sliceCoordinates = [
                 [self.regionSlice[1].start, self.regionSlice[1].stop],
                 [self.regionSlice[2].start, self.regionSlice[2].stop],
             ]
             sc = self.sliceCoordinates
             self.sliceEdges = [sc[0][1] - sc[0][0], sc[1][1] - sc[1][0]]
             ##print(self.regionSlice, sc, self.sliceEdges)
-            if self.detectorInfo.dimension == 2: ## remap to be 2d
+            if self.detectorInfo.dimension == 2:  ## remap to be 2d
                 self.regionSlice = self.regionSlice[1:3]
                 print("remapping regionSlice to be 2d")
 
@@ -401,13 +406,14 @@ def setupOutputDirString(self, analysisType):
             print("output dir: " + self.outputDir)
             logger.info("output dir: " + self.outputDir)
 
-
     def setupConfigHash(self):
         ## info to write to h5 to help processing
-        self.configHash = {"sliceCoordinates":self.sliceCoordinates,
-                           "analyzedModules": self.analyzedModules,
-                           "modules": self.detectorInfo.nModules,
-                           "rows": self.detectorInfo.nRows,
-                           "cols": self.detectorInfo.nCols
-                           }
+        self.configHash = {
+            "sliceCoordinates": self.sliceCoordinates,
+            "analyzedModules": self.analyzedModules,
+            "modules": self.detectorInfo.nModules,
+            "rows": self.detectorInfo.nRows,
+            "cols": self.detectorInfo.nCols,
+        }
+
     #### End of setup related functions ####

config_files/asc_epixMSuiteConfig.py

@@ -24,10 +24,10 @@
 
 experimentHash = {
     "detectorType": "epixm",
-    "detectorVersion":1,## new firmware
+    "detectorVersion": 1,  ## new firmware
     "exp": "ascdaq18",
     # "exp": "rixx1003721",
-    "location": "DetLab",## I guess
+    "location": "DetLab",  ## I guess
     "ignoreEventCodeCheck": True,
     "analyzedModules": [0, 1, 2, 3],
     "seedCut": 40,  ## pure guess

config_files/epix100SuiteConfig.py

@@ -40,7 +40,7 @@
     # 'ROIs':['roiFromSwitched_e557_rmfxx1005021']
     # 'ROIs':['allHRasicPixels', 'goodboxROI']#'roiAbove7k_raw_r123']
     # "ROIs": ["../data/XavierV4_2", "../data/OffXavierV4_2"],
-    #],
-    ##"regionSlice": np.s_[0:1, 0:704:, 0:768]  
-    "regionSlice": np.s_[0:1, 0:704:, 0:768]  
+    # ],
+    ##"regionSlice": np.s_[0:1, 0:704:, 0:768]
+    "regionSlice": np.s_[0:1, 0:704:, 0:768],
 }

config_files/epix10kQuadSuiteConfig.py

@@ -41,7 +41,7 @@
     # 'ROIs':['roiFromSwitched_e557_rmfxx1005021']
     # 'ROIs':['allHRasicPixels', 'goodboxROI']#'roiAbove7k_raw_r123']
     # "ROIs": ["../data/XavierV4_2", "../data/OffXavierV4_2"],
-    #],
-    ##"regionSlice": np.s_[0:1, 0:704:, 0:768]  
-    "regionSlice": np.s_[0:4, 0:352:, 0:384]  
+    # ],
+    ##"regionSlice": np.s_[0:1, 0:704:, 0:768]
+    "regionSlice": np.s_[0:4, 0:352:, 0:384],
 }