Merge branch 'development' into beamtime_testing_script

calibrationSuite/ancillaryMethods.py

@@ -53,15 +53,17 @@ def selectedClusters(clusters, row, col, lowEnerygCut, highEnergyCut, nPixelCut=
     pass
 
 
-def goodClusters(clusters, row, col, nPixelCut=4, isSquare=None):
-    ##print(clusters)
-    pixelRowCol = np.bitwise_and((clusters[:, :, 1] == row), (clusters[:, :, 2] == col))
+def goodClusters(clusters, module, row, col, nPixelCut=4, isSquare=None):
+    mCut = clusters[:,:,1] == module
+    pixelRowCol = np.bitwise_and((clusters[:, :, 2] == row), (clusters[:, :, 3] == col))
     if isSquare is None:
-        small = clusters[:, :, 3] < nPixelCut
+        small = clusters[:, :, 4] < nPixelCut
     else:
-        small = np.bitwise_and((clusters[:, :, 3] < nPixelCut), (clusters[:, :, 4] == isSquare))
-    return clusters[np.bitwise_and(small, pixelRowCol)]
-
+        small = np.bitwise_and((clusters[:, :, 4] < nPixelCut), (clusters[:, :, 5] == isSquare))
+    c = clusters[np.bitwise_and.reduce([mCut, small, pixelRowCol])]
+    ##print(c.shape)
+    ##print(c)
+    return c
 
 def getClusterEnergies(clusters):
     ##print(clusters)

calibrationSuite/argumentParser.py

@@ -21,10 +21,16 @@ def __init__(self):
         self.parser.add_argument("-r", "--run", type=int, help="run")
         self.parser.add_argument("-R", "--runRange", help="run range, format ...")
         self.parser.add_argument("--fivePedestalRun", type=int, help="5 pedestal run")
-        self.parser.add_argument("--fakePedestal", type=str, help="fake pedestal file")
+        self.parser.add_argument("--fakePedestalFile", type=str, help="fake pedestal file")
+        self.parser.add_argument("--g0PedFile", type=str, help="g0 pedestal file")
+        self.parser.add_argument("--g1PedFile", type=str, help="g1 pedestal file")
+        self.parser.add_argument("--g0GainFile", type=str, help="g0 gain file")
+        self.parser.add_argument("--g1GainFile", type=str, help="g1 gain file")
+        self.parser.add_argument("--offsetFile", type=str, help="offset file for stitching")
         self.parser.add_argument("-c", "--camera", type=int, help="camera.n")
         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("--mode", type=str, help="detector mode (1d, 2d, ...?") ## might be discoverable otherwise
         self.parser.add_argument(
             "-d", "--detType", type=str, default="", help="Epix100, Epix10ka, Epix10kaQuad, Epix10ka2M, ..."
         )