Merge branch 'main' into development

calibrationSuite/psana2Base.py

@@ -97,6 +97,7 @@ def setupPsana(self):
         try:
             self.step_value = self.myrun.Detector("step_value")
             self.step_docstring = self.myrun.Detector("step_docstring")
+            ##print('foo', self.step_value, self.step_docstring)
         except:
             self.step_value = self.step_docstring = None
 
@@ -297,11 +298,12 @@ def getScanValue(self, step, useStringInfo=False):
         ##print(self.step_value(step),self.step_docstring(step),useStringInfo)
         if useStringInfo:
             payload = self.step_docstring(step)
-            ##print(payload)
+            print(payload)
             sv = eval(payload.split()[-1][:-1])
+            ##print('sv', sv)
             print("step", int(self.step_value(step)), sv)
             logger.info("step" + str(int(self.step_value(step))) + str(sv))
-            return sv
+            return int(float(sv))
         return self.step_value(step)
 
     def plainGetRawData(self, evt):

setup.sh

@@ -7,11 +7,9 @@ current_dir=$(pwd)
 export PYTHONPATH="$PYTHONPATH:$current_dir"
 
 # so output folders are written in a shared location
-#export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1003721/results/scripts/"
-export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1005922/scratch/"
 echo "export OUTPUT_ROOT="\"$OUTPUT_ROOT\"
 
 # point to which config file to use
 #export SUITE_CONFIG="rixSuiteConfig.py"
 export SUITE_CONFIG="epixMSuiteConfig.py"
-echo "export SUITE_CONFIG="\"$SUITE_CONFIG\"
+echo "export SUITE_CONFIG="\"$SUITE_CONFIG\"

standalone_scripts/simpler_epixhr.py

@@ -19,6 +19,7 @@
 ds = DataSource(exp="%s" % (expt), run=run)
 myrun = next(ds.runs())
 det = myrun.Detector("epixhr")
+det = myrun.Detector("epixm")
 
 
 from psmon import publish

suite_scripts/AnalyzeH5.py

@@ -40,7 +40,8 @@ def __init__(self):
         self.files = args.files.replace(" ", "")
         print(self.files)
         self.outputDir = args.path
-        logging.info("Output dir: " + self.outputDir)
+        print("output dir:", self.outputDir)
+        ##logging.info("Output dir: " + self.outputDir)
         self.label = args.label
         self.camera = 0
 
@@ -55,6 +56,7 @@ def identifyAnalysis(self):
         try:
             self.analysisType = self.h5Files[0]["analysisType"]
             self.sliceCoordinates = self.h5Files[0]["sliceCoordinates"][()]
+            print('slice coordinates:', self.sliceCoordinates)
         except:
             ## do something useful here, maybe
             self.analysisType = None
@@ -82,13 +84,13 @@ def clusterAnalysis(self):
         except:
             pass
 
-        self.nBins = 100
+        self.nBins = 200## for epixM with a lot of 2 photon events...
         self.lowEnergyCut = 4  ## fix - should be 0.5 photons or something
         self.highEnergyCut = 15  ## fix - should be 1.5 photons or something
         ##tmp
         npyFileName = "%s/r%d_clusters.npy" % (self.outputDir, self.run)
         np.save(npyFileName, clusters)
-        logger.info("Wrote file: " + npyFileName)
+        ##logger.info("Wrote file: " + npyFileName)
 
         self.analyzeSimpleClusters(clusters)
 
@@ -148,7 +150,7 @@ def analyzeSimpleClusters(self, clusters):
 
         rows = self.sliceEdges[0]
         cols = self.sliceEdges[1]
-        m = 1## temp hack
+        m = 1## temp hack, Kaz's favorite asic, off by 1
         fitInfo = np.zeros((maximumModule, rows, cols, 5))  ## mean, std, area, mu, sigma
         for i in range(rows):
             for j in range(cols):
@@ -176,7 +178,7 @@ def analyzeSimpleClusters(self, clusters):
                 plt.figtext(0.7, 0.8, "%d entries (peak)" % (area))
                 plt.figtext(0.7, 0.75, "mu %0.2f" % (mu))
                 plt.figtext(0.7, 0.7, "sigma %0.2f" % (sigma))
-                figFileName = "%s/%s_m%d_r%d_c%d_r%d_c%d_%s_E.png" % (
+                figFileName = "%s/%s_r%d_c%d_m%d_r%d_c%d_%s_E.png" % (
                     self.outputDir,
                     self.__class__.__name__,
                     self.run,

suite_scripts/LinearityPlotsParallelSlice.py

@@ -27,12 +27,12 @@
 class LinearityPlotsParallel(BasicSuiteScript):
     def __init__(self):
         super().__init__("scan")  ##self)
-        self.saturated = [True, False][0]
+        self.saturated = [True, False][1]
         print("using saturation fit =", self.saturated)
         logger.info("using saturation fit =" + str(self.saturated))
         self.residuals = [True, False][0]
         self.profiles = [True, False][1]
-        self.seabornProfiles = [True, False][1]
+        self.seabornProfiles = [True, False][0]
         try:
             print("positive events:", "positive" in self.special)
             logger.info("positive events:" + str("positive" in self.special))
@@ -172,8 +172,8 @@ def analyze_h5(self, dataFile, label):
         lpp.plotDataROIs(rois.T, fluxes, "ROIs")
 
     def analyze_h5_slice(self, dataFile, label):
-        module = 0
-        nModules = 1
+        module = 2
+        nModules = 3
         data = h5py.File(dataFile)
         fluxes = data["fluxes"][()]
         pixels = data["slice"][()]
@@ -185,15 +185,16 @@ def analyze_h5_slice(self, dataFile, label):
         for i in range(rows):
             for j in range(cols):
                 iDet, jDet = self.sliceToDetector(i, j)
-                self.fitInfo[module, i, j, 8] = self.g0Ped[module, iDet, jDet]
-                self.fitInfo[module, i, j, 9] = self.g1Ped[module, iDet, jDet]
-                self.fitInfo[module, i, j, 10] = self.g0Gain[module, iDet, jDet]
-                self.fitInfo[module, i, j, 11] = self.g1Gain[module, iDet, jDet]
-                self.fitInfo[module, i, j, 12] = self.offset[module, iDet, jDet]
-                g0 = pixels[:, i, j] < lpp.g0cut
+                if False:
+                    self.fitInfo[module, i, j, 8] = self.g0Ped[module, iDet, jDet]
+                    self.fitInfo[module, i, j, 9] = self.g1Ped[module, iDet, jDet]
+                    self.fitInfo[module, i, j, 10] = self.g0Gain[module, iDet, jDet]
+                    self.fitInfo[module, i, j, 11] = self.g1Gain[module, iDet, jDet]
+                    self.fitInfo[module, i, j, 12] = self.offset[module, iDet, jDet]
+                g0 = pixels[:, module, i, j] < lpp.g0cut
                 g1 = np.logical_not(g0)
                 if len(g0[g0]) > 2:
-                    y = np.bitwise_and(pixels[:, i, j][g0], lpp.gainBitsMask)
+                    y = np.bitwise_and(pixels[:, module, i, j][g0], lpp.gainBitsMask)
                     y_g0_max = y.max()
                     x = fluxes[g0]
                     if self.profiles:
@@ -208,6 +209,8 @@ def analyze_h5_slice(self, dataFile, label):
                         ##np.save("temp_r%dc%d_x.py" %(i,j), fluxes[g0])
                         ##np.save("temp_r%dc%d_y.py" %(i,j), y)
                         ##np.save("temp_r%dc%d_func.py" %(i,j), fitFunc)
+                        ##print(fitInfo.shape)
+                        ##print(fitPar)
                         self.fitInfo[module, i, j, 0:2] = fitPar[0:2]  ## indices for saturated case
                         self.fitInfo[module, i, j, 2] = r2
                         self.fitInfo[module, i, j, 6] = y_g0_max
@@ -226,7 +229,7 @@ def analyze_h5_slice(self, dataFile, label):
                                 plt.figure(1)
 
                 if len(g1[g1]) > 2:
-                    y = np.bitwise_and(pixels[:, i, j][g1], lpp.gainBitsMask)
+                    y = np.bitwise_and(pixels[:, module, i, j][g1], lpp.gainBitsMask)
                     y_g1_min = y.min()
                     x = fluxes[g1]
                     if self.profiles:
@@ -372,7 +375,7 @@ def analyze_h5_slice(self, dataFile, label):
             fluxes=flux,
             rois=np.array(roiMeans),
             pixels=np.array(singlePixelData),
-            slice=rawFrames[0][lpp.regionSlice],
+            slice=rawFrames[lpp.regionSlice]
         )
 
         nGoodEvents += 1
@@ -410,6 +413,7 @@ def analyze_h5_slice(self, dataFile, label):
         logger.info("Wrote file: " + fileName)
 
     if False:
+        print("this is broken")
         label = "rawInTimeDot"
         if doKazFlux:
             label = "raw_smarterPoints"

suite_scripts/SimpleClustersParallelSlice.py

@@ -128,7 +128,7 @@ def analyze_h5(self, dataFile, label):
     smd = sic.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (sic.outputDir, sic.className, sic.camera, sic.run, size))
 
     ## 50x50 pixels, 3x3 clusters, 10% occ., 2 sensors
-    maxClusters = int(50 * 50 / 3 / 3 * 0.1 * 2)
+    maxClusters = 1000##int(50 * 50 / 3 / 3 * 0.1 * 2)
     try:
         seedCut = sic.detectorInfo.seedCut
     except:

suite_scripts/TimeScanParallelSlice.py

@@ -29,14 +29,16 @@ def __init__(self):
             pass
 
     def plotData(self, rois, pixels, delays, label):
+##        print(type(delays))
+##        print('delays here:', delays)
         for i, roi in enumerate(self.ROIs):
             ax = plt.subplot()
             ax.plot(delays, rois[i], label=self.ROIfileNames[i])
             plt.grid(which="major", linewidth=0.5)
             minor_locator = AutoMinorLocator(5)
             ax.xaxis.set_minor_locator(minor_locator)
             plt.grid(which="minor", linewidth=0.5)
-            plt.xlabel("Time delay (Ticks)")
+            plt.xlabel("Time delay (Ticks/1000)")
             # plt.ylabel('Step Mean (keV)')
             plt.ylabel("Step Mean (ADU)")
             plt.grid(which="major", linewidth=0.75)
@@ -56,7 +58,7 @@ def plotData(self, rois, pixels, delays, label):
             minor_locator = AutoMinorLocator(5)
             ax.xaxis.set_minor_locator(minor_locator)
             plt.grid(which="minor", linewidth=0.5)
-            plt.xlabel("Time delay (Ticks)")
+            plt.xlabel("Time delay (Ticks/1000)")
             # plt.ylabel('Step Mean (keV)')
             plt.ylabel("Step Mean (ADU)")
             ##plt.yscale('log')
@@ -76,7 +78,7 @@ def plotData(self, rois, pixels, delays, label):
             minor_locator = AutoMinorLocator(5)
             ax.xaxis.set_minor_locator(minor_locator)
             plt.grid(which="minor", linewidth=0.5)
-            plt.xlabel("Delay (Ticks)")
+            plt.xlabel("Delay (Ticks/1000)")
             plt.ylabel("Pixel ADU")
 
             figFileName = "%s/%s_r%d_c%d_%s_pixel%d.png" % (self.outputDir, self.__class__.__name__, self.run, self.camera, label, i)
@@ -119,10 +121,14 @@ def analyze_h5(self, dataFile, norm, label):
 
         a = h5py.File(dataFile)[norm]
         delays = np.array([k for k in a.keys()])
-        delays = delays.astype("int")
+        print(delays)
+        ##delays = delays.astype('float').astype("int")
+        ##delays = delays.astype('float').astype("int")
         delays.sort()
         d = np.array([a[str(k)] for k in delays])
         delays = np.array([d for d in delays])
+        delays = [eval(d)/1000. for d in delays]
+        ##delays /= 1000.
         print(delays)
 
         runString = "_r%d" % (self.run)
@@ -168,7 +174,7 @@ def analyze_h5(self, dataFile, norm, label):
     offset = len(tsp.ROIs)
 
     stepGen = tsp.getStepGen()
-    ##    for nstep, step in enumerate (tsp.ds.steps()):
+    ##for nstep, step in enumerate (tsp.ds.steps()):
     for nstep, step in enumerate(stepGen):
         ##scanValue = tsp.getScanValue(step, useStringInfo=True)
         scanValue = tsp.getScanValue(step, True)
@@ -193,12 +199,12 @@ def analyze_h5(self, dataFile, norm, label):
 
                 ##tsp.isBeamEvent(evt):
                 if tsp.detectorInfo.detectorType == 'epixm' or tsp.isBeamEvent(evt):##FEE hack
-                    frames = tsp.getRawData(evt, gainBitsMasked=True)
+                    frames = tsp.getRawData(evt)##, gainBitsMasked=True)
                     ##print("real beam on event", nstep, nevt)
                     ##logger.info("real beam on event" + str(nstep) + ", " + str(nevt))
                 elif tsp.use_281_for_old_data and ec[281]:
-                    frames = tsp.getRawData(evt, gainBitsMasked=True)
-                    ##print("281 only...")
+                    frames = tsp.getRawData(evt)##, gainBitsMasked=True)
+                    print("281 only...")
                 elif ec[137]:
                     tsp.flux = tsp._getFlux(evt) ## fix this
                     continue
@@ -208,7 +214,7 @@ def analyze_h5(self, dataFile, norm, label):
                     continue
             else:
                 tsp.flux = tsp._getFlux(evt)  ## fix this
-                frames = tsp.getRawData(evt, gainBitsMasked=True)
+                frames = tsp.getRawData(evt)##, gainBitsMasked=True)
 
             if frames is None:
                 ##print("no frame")

suite_scripts/epixMSuiteConfig.py

@@ -12,28 +12,32 @@
 ##experimentHash = {'exp':'mfxx1005021', 'location':'MfxEndstation', 'fluxSource':'MFX-USR-DIO', 'fluxChannels':[11], 'fluxSign':-1}
 ##experimentHash = {'exp':'rixc00121', 'location':'RixEndstation',
 singlePixelArray = []
-for i in range(4):
+for i in range(1,3):
     singlePixelArray.append([i, 10, 10])    
     singlePixelArray.append([i, 10, 100])
     singlePixelArray.append([i, 100, 10])
     singlePixelArray.append([i, 100, 100])
+    singlePixelArray.append([i, 150, 150])
+    singlePixelArray.append([i, 80, 20])
+
+singlePixelArray.append([2, 178, 367])
 
 experimentHash = {
     "detectorType": "epixm",
-    ##"exp": "rixx1005922",
-    "exp": "rixx1003721",
+    "exp": "rixx1005922",
+    ##"exp": "rixx1003721",
     "location": "RixEndstation",
     "analyzedModules":[1,2],
     "seedCut":40, ## pure guess
     "neighborCut":10, ##pure guess
     "fluxSource": "MfxDg1BmMon",
-    'fluxChannels':[8, 14],
+    'fluxChannels':[11],
     "fluxSign": -1,
     "singlePixels": singlePixelArray,
     #                  'ROIs':['module0', 'module2', 'module4', 'module6', 'module10','module12', 'module14']
     #                  'ROIs':['roiFromSwitched_e557_rmfxx1005021']
     ##                  'ROIs':['allHRasicPixels', 'goodboxROI']#'roiAbove7k_raw_r123']
     ##"ROIs": ["../data/XavierV4_2", "../data/OffXavierV4_2"],
-    "ROIs": ["../data/smallRegionFourAsics.npy"],
-    "regionSlice": np.s_[0:4, 40:60:, 170:200],## random
+    "ROIs": ["../data/cometPinhole.npy", "../data/smallRegionFourAsics.npy", "../data/smallRegionTwoAsicsForBhavna.npy"],
+    "regionSlice": np.s_[0:4, 150:180:, 340:368],## small region near Kaz rec
 }

suite_scripts/simplePhotonCounter.py

@@ -51,10 +51,11 @@ def __init__(self):
         if evt is None:
             break
         if not spc.isBeamEvent(evt):
-            print('foo')
+            ##print('foo')
             continue
 
         if spc.fakePedestal is not None:
+            rawFrames = spc.getRawData(evt)
             frames = rawFrames.astype("float") - spc.fakePedestal
             frames /= gain ## psana may not have the right default
         else: