Merge pull request #128 from slaclab/epix10k_psana1

Epix10k psana1

calibrationSuite/basicSuiteScript.py

@@ -95,6 +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))
+                return None
+        except:
+            self.nZero = 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

@@ -42,11 +42,11 @@ def __init__(self, detType, detSubtype="1d", detVersion=0):
 
         knownTypes = ["epixhr", "epixm", "epix100", "Epix100a",
                       "jungfrau", "Jungfrau",## cxic00121 has no alias in run 88
-                      "epix10k", "archon"]
+                      "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.epix10kCameraTypes = {1: "Epix10ka", 4: "Epix10kaQuad", 16: "Epix10ka2M"}
         self.jungfrauCameraTypes = {1: "Jungfrau0.5", 2: "Jungfrau1M", 8: "Jungfrau4M"}
 
     def setupDetector(self): ## needs nModules to be set
@@ -145,6 +145,23 @@ def setup_jungfrau(self):
         self.seedCut = 3
         self.neighborCut = 0.5  
 
+    def setup_epix10k(self):
+        self.cameraType = self.epix10kCameraTypes[self.nModules]
+        self.g0cut = 1 << 14
+        self.nRows = 352
+        self.nCols = 384
+        self.nColsPerBank = 96
+        self.nBanksRow = int(self.nCols / self.nColsPerBank)
+        self.nBanksCol = 2
+        self.nRowsPerBank = int(self.nRows / self.nBanksCol)
+        # need to still implement getGainMode()
+        # self.gainMode = self.getGainMode()
+        self.preferredCommonMode = "colCommonMode"
+        self.clusterShape = [3, 3]
+        self.aduPerKeV = 16 ## high gain; 5.5 for medium
+        self.seedCut = 3
+        self.neighborCut = 0.5  
+
     def setup_rixsCCD(self):
         print("rixsCCD mode:", self.detectorSubtype)
         self.cameraType = "rixsCCD" ##+ mode ## psana should support mode

calibrationSuite/psana1Base.py

@@ -44,7 +44,10 @@ 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.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())
@@ -149,7 +152,7 @@ def getCalibData(self, evt):
         return self.det.calib(evt)
 
     def getImage(self, evt, data=None):
-        return self.raw.image(evt, data)
+        return self.det.image(evt, data)
 
     def getPedestal(self, evt, gainmode):
         if self.detectorInfo.autoRanging:

calibrationSuite/psanaCommon.py

@@ -249,7 +249,7 @@ def setupFromCmdlineArgs(self):
 
         self.loadPedestalGainOffsetFiles()
 
-        print("det type:", self.args.detType)
+        print("command line det type:", self.args.detType)
         if self.args.detType == "":
             if self.args.nModules is not None:
                 self.detectorInfo.setNModules(self.args.nModules)

config_files/epix10kQuadSuiteConfig.py

@@ -21,7 +21,8 @@
     singlePixelArray.append([i, 80, 20])
 
 experimentHash = {
-    "detectorType": "Epix10kaQuad",
+    ##"detectorType": "Epix10kaQuad",## this needs work
+    "detectorType": "Epix10ka",
     "exp": "detdaq21",
     # "exp": "rixx1003721",
     "location": "DetLab",

config_files/epixMSuiteConfig.py

@@ -12,22 +12,20 @@
 # experimentHash = {'exp':'mfxx1005021', 'location':'MfxEndstation', 'fluxSource':'MFX-USR-DIO', 'fluxChannels':[11], 'fluxSign':-1}
 # experimentHash = {'exp':'rixc00121', 'location':'RixEndstation',
 singlePixelArray = []
-for i in range(1, 3):
+for i in range(0, 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])
+    singlePixelArray.append([i, 180, 10])
+    singlePixelArray.append([i, 10, 200])
+    singlePixelArray.append([i, 180, 200])
+    singlePixelArray.append([i, 10, 380])
+    singlePixelArray.append([i, 180, 380])
 
 experimentHash = {
     "detectorType": "epixm",
+    "detectorVersion":1,## new firmware
     "exp": "rixx1005922",
-    # "exp": "rixx1003721",
     "location": "RixEndstation",
-    "analyzedModules": [1, 2],
+    "analyzedModules": [0, 2, 3],
     "seedCut": 40,  ## pure guess
     "neighborCut": 10,  ##pure guess
     # "fluxSource": "MfxDg1BmMon",

config_files/epixM_oldCamera_SuiteConfig.py

@@ -0,0 +1,49 @@
+##############################################################################
+## This file is part of 'SLAC Beamtime Calibration Suite'.
+## It is subject to the license terms in the LICENSE.txt file found in the
+## top-level directory of this distribution and at:
+##    https://confluence.slac.stanford.edu/display/ppareg/LICENSE.html.
+## No part of 'SLAC Beamtime Calibration Suite', including this file,
+## may be copied, modified, propagated, or distributed except according to
+## the terms contained in the LICENSE.txt file.
+##############################################################################
+import numpy as np
+
+# experimentHash = {'exp':'mfxx1005021', 'location':'MfxEndstation', 'fluxSource':'MFX-USR-DIO', 'fluxChannels':[11], 'fluxSign':-1}
+# experimentHash = {'exp':'rixc00121', 'location':'RixEndstation',
+singlePixelArray = []
+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",
+    "location": "RixEndstation",
+    "analyzedModules": [1, 2],
+    "seedCut": 40,  ## pure guess
+    "neighborCut": 10,  ##pure guess
+    # "fluxSource": "MfxDg1BmMon",
+    "fluxSource": "MfxDg2BmMon",
+    "fluxChannels": [15],
+    "fluxSign": 1,  ## for dg2
+    # "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/cometPinhole.npy",
+        "../data/smallRegionFourAsics.npy",
+        "../data/smallRegionTwoAsicsForBhavna.npy",
+    ],
+    "regionSlice": np.s_[0:4, 0:192:, 0:384],  ## small region near Kaz rec
+}

setup.sh

@@ -10,11 +10,11 @@ echo "PYTHONPATH = $PYTHONPATH"
 
 # so output folders are written in a shared location
 ##export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1005922/scratch/"
-##export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1005922/results/"
-export OUTPUT_ROOT="/sdf/data/lcls/ds/det/detdaq21/results/"
+export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1005922/results/"
+##export OUTPUT_ROOT="/sdf/data/lcls/ds/det/detdaq21/results/"
 echo "OUTPUT_ROOT = $OUTPUT_ROOT"
 
 # point to which config file to use
-##export SUITE_CONFIG="$git_project_root_dir/config_files/epixMSuiteConfig.py"
-export SUITE_CONFIG="$git_project_root_dir/config_files/epix100SuiteConfig.py"
+export SUITE_CONFIG="$git_project_root_dir/config_files/epixMSuiteConfig.py"
+##export SUITE_CONFIG="$git_project_root_dir/config_files/epix100SuiteConfig.py"
 echo "SUITE_CONFIG = $SUITE_CONFIG"

setup_epix100.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+# Setup environment variables
+
+
+# current_dir=$(pwd)
+git_project_root_dir=$(git rev-parse --show-toplevel)
+# so scripts can find the calibrationSuite library code
+export PYTHONPATH="$PYTHONPATH:$git_project_root_dir"
+echo "PYTHONPATH = $PYTHONPATH"
+
+# so output folders are written in a shared location
+##export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1005922/scratch/"
+##export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1005922/results/"
+export OUTPUT_ROOT="/sdf/data/lcls/ds/det/detdaq21/results/"
+echo "OUTPUT_ROOT = $OUTPUT_ROOT"
+
+# point to which config file to use
+##export SUITE_CONFIG="$git_project_root_dir/config_files/epixMSuiteConfig.py"
+export SUITE_CONFIG="$git_project_root_dir/config_files/epix100SuiteConfig.py"
+echo "SUITE_CONFIG = $SUITE_CONFIG"

setup_epix10k.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+# Setup environment variables
+
+
+# current_dir=$(pwd)
+git_project_root_dir=$(git rev-parse --show-toplevel)
+# so scripts can find the calibrationSuite library code
+export PYTHONPATH="$PYTHONPATH:$git_project_root_dir"
+echo "PYTHONPATH = $PYTHONPATH"
+
+# so output folders are written in a shared location
+##export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1005922/scratch/"
+##export OUTPUT_ROOT="/sdf/data/lcls/ds/rix/rixx1005922/results/"
+export OUTPUT_ROOT="/sdf/data/lcls/ds/det/detdaq21/results/"
+echo "OUTPUT_ROOT = $OUTPUT_ROOT"
+
+# point to which config file to use
+##export SUITE_CONFIG="$git_project_root_dir/config_files/epixMSuiteConfig.py"
+export SUITE_CONFIG="$git_project_root_dir/config_files/epix10kQuadSuiteConfig.py"
+echo "SUITE_CONFIG = $SUITE_CONFIG"

suite_scripts/CalcNoiseAndMean.py

@@ -184,5 +184,6 @@
     bss.dumpEventCodeStatistics()
     ## temp for Alex:
     if False:
+    ##if True:
         np.save("nonZeroAsicAccounting.npy", np.array(nonZeroAsicArray))
         print("non-zero asic accounting:", nonZeroAsicArray)

suite_scripts/simplePhotonCounter.py

@@ -104,7 +104,7 @@
     print("total photons in detector using cut %0.2f is %0.3f" % (spc.photonCut, (thresholded).sum()))
     logger.info("total photons in detector using cut %0.2f is %0.3f" % (spc.photonCut, (thresholded).sum()))
 
-    if False:
+    if True:##False:
         spectrumFileName = "%s/%s_%s_r%d_c%d_%s_spectrum.npy" % (
             spc.outputDir,
             scriptType,
@@ -115,4 +115,14 @@
         )
         np.save(spectrumFileName, energyHistogram)
 
+        imageFileName = spectrumFileName.replace("spectrum", "image")
+        tImage = spc.getImage(evt, thresholded)
+        np.save(imageFileName, tImage)
+        import matplotlib.pyplot as plt
+        p90 = np.percentile(tImage, 90)
+        print("clipping image at 90% of max")
+        plt.imshow(tImage.clip(0, p90))
+        plt.colorbar()
+        plt.savefig(imageFileName.replace("npy", "png"))
+
     spc.dumpEventCodeStatistics()