Merge pull request #138 from slaclab/development

Merge Code From Beamtime October 1st 2024

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
@@ -60,6 +62,9 @@ def __init__(self):
         self.parser.add_argument("--fluxCutMax", type=float, help="maximum flux to be included in analysis")
         self.parser.add_argument("--seedCut", help="seed cut for clustering")
         self.parser.add_argument("--photonEnergy", type=float, help="photon energy")
+        self.parser.add_argument("--aduPerKeV", type=float, help="ADU per keV")
+        self.parser.add_argument("--gainMode", type=int, help="gain mode (int)")
+
         self.parser.add_argument(
             "--special",
             type=str,

calibrationSuite/basicSuiteScript.py

@@ -95,17 +95,22 @@ 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))
 
+            try:
+                self.dumpEpixMHeaderInfo(evt)
+            except:
+                pass
+
         if False and self.special:  ## turned off for a tiny bit of speed
             if "thirteenBits" in self.special:
                 frames = frames & 0xFFFE
@@ -231,9 +236,9 @@ def rowCommonModeCorrection(self, frame, arbitraryCut=1000):
                             frame[r, colOffset : colOffset + self.detectorInfo.nColsPerBank] < arbitraryCut
                         ]
                     )
-                    frame[r, colOffset : colOffset + self.detectorInfo.nColsPerBank] -= rowCM
+                    if not np.isnan(rowCM): ## no pixels found under cut
+                        frame[r, colOffset : colOffset + self.detectorInfo.nColsPerBank] -= rowCM
                 except Exception:
-                    rowCM = -666
                     print("rowCM problem")
                     logger.error("rowCM problem")
                     print(frame[r, colOffset : colOffset + self.detectorInfo.nColsPerBank])
@@ -245,6 +250,7 @@ def colCommonModeCorrection(self, frame, arbitraryCut=1000):
         ## cut keeps photons in common mode - e.g. set to <<1 photon
 
         ##rand = np.random.random()
+
         for c in range(self.detectorInfo.nCols):
             rowOffset = 0
             for b in range(0, self.detectorInfo.nBanksRow):
@@ -254,9 +260,12 @@ def colCommonModeCorrection(self, frame, arbitraryCut=1000):
                             frame[rowOffset : rowOffset + self.detectorInfo.nRowsPerBank, c] < arbitraryCut
                         ]
                     )
-                    frame[rowOffset : rowOffset + self.detectorInfo.nRowsPerBank, c] -= colCM
+                    if not np.isnan(colCM): ## if no pixels < cut we get nan
+                        if False:
+                            if c<100:
+                                self.commonModeVals.append(colCM)
+                        frame[rowOffset : rowOffset + self.detectorInfo.nRowsPerBank, c] -= colCM
                 except Exception:
-                    colCM = -666
                     print("colCM problem")
                     logger.error("colCM problem")
                     print(frame[rowOffset : rowOffset + self.detectorInfo.nRowsPerBank], c)

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()
@@ -156,5 +158,5 @@ def getImage(self, evt, data=None):
 
     def getPedestal(self, evt, gainmode):
         if self.detectorInfo.autoRanging:
-            return self.det.pedestal(evt)[gainmode]
+            return self.det.pedestals(evt)[gainmode]
         return self.det.pedestals(evt)

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
 
@@ -255,17 +255,24 @@ 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]
         delta = evensEvenRowsOddsOddRows.mean() - oddsEvenRowsEvensOddRows.mean()
         ##print("delta:", delta)
         return delta > 0
+
+    def dumpEpixMHeaderInfo(self, evt):
+        print(f'frameNo: {self.det.raw.frameNo(evt)},',
+              f'asicNo: {self.det.raw.asicNo(evt)},',
+              f'autoFillMask: {[hex(a) for a in self.det.raw.autoFillMask(evt)]},',
+              f'fixedMask: {self.det.raw.fixedMask(evt)}')
+