Merge pull request #117 from slaclab/beamtime_june_14_2024

Merge in changes from beamtime june 14 2024
slaclab · Jun 17, 2024 · 8bb92fd · 8bb92fd
2 parents 79edd92 + 0e4bd70
commit 8bb92fd
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Showing 5 changed files with 28 additions and 9 deletions.
diff --git a/calibrationSuite/argumentParser.py b/calibrationSuite/argumentParser.py
@@ -53,7 +53,8 @@ def __init__(self):
         self.parser.add_argument("-cf", "--configFile", type=str, help="config file path, can be relative or full path")
         self.parser.add_argument("-L", "--label", type=str, help="analysis label")
         self.parser.add_argument("-t", "--threshold", help="threshold (ADU or keV or wave8) depending on --detObj")
-        self.parser.add_argument("--fluxCut", type=float, help="minimum flux to be included in analysis")
+        self.parser.add_argument("--fluxCutMin", type=float, help="minimum flux to be included in analysis")
+        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(
             "--special",

diff --git a/calibrationSuite/basicSuiteScript.py b/calibrationSuite/basicSuiteScript.py
@@ -180,8 +180,10 @@ def __init__(self, analysisType="scan"):
             self.seedCut = eval(self.args.seedCut)
         else:
             self.seedCut = None
-        if self.args.fluxCut is not None:
-            self.fluxCut = self.args.fluxCut
+        if self.args.fluxCutMin is not None:
+            self.fluxCutMin = self.args.fluxCutMin
+        if self.args.fluxCutMax is not None:
+            self.fluxCutMax = self.args.fluxCutMax
         try:
             self.runRange = eval(self.args.runRange)  ## in case needed
         except Exception:

diff --git a/calibrationSuite/psana1Base.py b/calibrationSuite/psana1Base.py
@@ -152,7 +152,12 @@ def getFlux(self, evt):
                 return None
             f = fluxes[self.fluxChannels].mean() * self.fluxSign
             try:
-                if f < self.fluxCut:
+                if f < self.fluxCutMin:
+                    return None
+            except Exception:
+                pass
+            try:
+                if f > self.fluxCutMax:
                     return None
             except Exception:
                 pass

diff --git a/calibrationSuite/psana2Base.py b/calibrationSuite/psana2Base.py
@@ -250,7 +250,12 @@ def _getFlux(self, evt):
             # print(e)
             return None
         try:
-            if f < self.fluxCut:
+            if f < self.fluxCutMin:
+                return None
+        except Exception:
+            pass
+        try:
+            if f > self.fluxCutMax:
                 return None
         except Exception:
             pass

diff --git a/suite_scripts/LinearityPlotsParallelSlice.py b/suite_scripts/LinearityPlotsParallelSlice.py
@@ -160,7 +160,7 @@ def plotDataROIs(self, means, flux, label, raw=True):
     def analyze_h5(self, dataFile, label):
         data = h5py.File(dataFile)
         fluxes = data["fluxes"][()]
-        print(fluxes)
+        print(np.array(fluxes))
         rois = data["rois"][()]
         pixels = data["pixels"][()]
         g0s = []
@@ -215,8 +215,11 @@ def analyze_h5_slice(self, dataFile, label):
                         break
 
                     iDet, jDet = self.sliceToDetector(i, j)
-                    if False:
+                    try:
                         self.fitInfo[module, i, j, 8] = self.g0Ped[module, iDet, jDet]
+                    except:
+                        pass
+                    if False:
                         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]
@@ -267,7 +270,7 @@ def analyze_h5_slice(self, dataFile, label):
                         y_g1_min = y.min()
                         x = fluxes[g1]
                         if self.profiles:
-                            x, y, err = ancillaryMethods.makeProfile(x, y, 50)
+                            x, y, err = ancillaryMethods.makeProfile(x, y, 50, myStatistic="median")
                             if x is None:  ##empty plot if single points/bin apparently
                                 print("empty profile for %d, %d" % (i, j))
                                 logger.info("empty profile for %d, %d" % (i, j))
@@ -370,7 +373,10 @@ def analyze_h5_slice(self, dataFile, label):
 
     lpp.setupPsana()
 
-    size = 666
+    try:
+        size = comm.Get_size()
+    except:
+        size = 1
     smd = lpp.ds.smalldata(
         filename="%s/%s_%s_c%d_r%d_n%d.h5" % (lpp.outputDir, lpp.className, lpp.label, lpp.camera, lpp.run, size)
     )