Merge pull request #145 from slaclab/beamtime_nov_8th_merge_dev

 Merge beamtime november 8 2024 branch into development

calibrationSuite/detectorInfo.py

@@ -112,7 +112,7 @@ def setup_epixUHR(self):
         self.preferredCommonMode = "clusterCommonMode"  ## not yet defined
         self.clusterShape = [3, 3]
         self.gainMode = None  ## high, medium, low, lower
-        self.aduPerKeV = 40 ## high gain; medium is down by 2.8
+        self.aduPerKeV = 3 ## high gain; medium is down by 2.8
         self.seedCut = 2
         self.neighborCut = 0.25  ## ditto
 

config_files/epixUHRSuiteConfig.py

@@ -15,18 +15,18 @@
 ##for i in [0, 2, 3]:##range(0, 3):
 ## for 41-c00-01
 m = 0
-for r in range(11, 60):
-    for c in range(49):
-        if r%12 == 0 and c%6 == 0:
+for r in range(109, 157):
+    for c in range(48):
+        if r%12 == 11 and c%6 == 0:
             singlePixelArray.append([m, r, c])
 singlePixelArray.append([m, 12*7, 60])
 singlePixelArray.append([m, 13*7, 60+12])
 singlePixelArray.append([m, 14*7, 60+24])
 
 m = 3
-for r in range(8, 57):
-    for c in range(10, 59):
-        if r%12 == 0 and c%6 == 0:
+for r in range(111, 159):
+    for c in range(10, 58):
+        if r%12 == 11 and c%6 == 0:
             singlePixelArray.append([m, r, c])
 singlePixelArray.append([m, 12*7, 60])
 singlePixelArray.append([m, 13*7, 60+12])
@@ -38,12 +38,13 @@
     ##"detectorVersion": 1,  ## new firmware
     "exp": "rixx1005922",
     "location": "RixEndstation",
-    "analyzedModules": [0, 1, 2, 3],
+    "analyzedModules": [0, 3],
     "seedCut": 40,  ## pure guess
     "neighborCut": 10,  ##pure guess
     "fluxSource": "MfxDg1BmMon",
     # "fluxSource": "MfxDg2BmMon",
-    "fluxChannels": [15],  ## or 11 if we see saturation
+    "fluxChannels": [11],  ## 8 Nov
+    ##"fluxChannels": range(0,16),  ## direct beam, 11 Nov?
     # "fluxSign": 1,  ## for dg2
     "fluxSign": -1,
     "singlePixels": singlePixelArray,

setup_epixUHR.sh

@@ -0,0 +1,18 @@
+#!/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/results/"
+echo "OUTPUT_ROOT = $OUTPUT_ROOT"
+
+# point to which config file to use
+export SUITE_CONFIG="$git_project_root_dir/config_files/epixUHRSuiteConfig.py"
+##export SUITE_CONFIG="$git_project_root_dir/config_files/epix100SuiteConfig.py"
+echo "SUITE_CONFIG = $SUITE_CONFIG"

standalone_scripts/cmCorrectAlexData.py

@@ -0,0 +1,94 @@
+import numpy as np
+import sys
+import matplotlib.pyplot as plt
+
+nCols = 384
+nRows = 192
+nBanksRow = 4
+nRowsPerBank = int(nRows/nBanksRow)
+
+
+def colCommonModeCorrection(frame, arbitraryCut=1000):
+    for c in range(nCols):
+        rowOffset = 0
+        for b in range(0, nBanksRow):
+            if True:
+                colCM = np.median(
+                    frame[rowOffset : rowOffset + nRowsPerBank, c][
+                        frame[rowOffset : rowOffset + nRowsPerBank, c] < arbitraryCut
+                    ]
+                )
+                if not np.isnan(colCM):  ## if no pixels < cut we get nan
+                    frame[rowOffset : rowOffset + nRowsPerBank, c] -= colCM.astype('int')
+            ##except Exception:
+            if False:
+                print("colCM problem")
+                print(frame[rowOffset : rowOffset + nRowsPerBank], c)
+            rowOffset += nRowsPerBank
+    return frame
+
+
+
+f = sys.argv[1]
+label = f.split('/')[-1]
+label = label.split('.')[0]
+rawData = np.load(f)
+data = np.zeros(rawData.shape)
+
+try:
+    signalPixel = eval(sys.argv[2])
+    darkPixel = eval(sys.argv[3])
+except:
+    print("defaulting to standard pixels")
+    signalPixel = (66, 66)
+    darkPixel = (6, 6)
+
+nSkipForChargeInjectionOffset = 200
+nInjections = 1024
+gainCut = 1<<15
+gainBitsMask = gainCut -1
+
+dataHighSignalPixel = data[signalPixel[0],signalPixel[1],:]<gainCut
+dataHighDarkPixel = data[darkPixel[0],darkPixel[1],:]<gainCut
+x = np.arange(nSkipForChargeInjectionOffset, nInjections)
+
+rawData &= gainBitsMask
+
+pedestal = rawData[:,:,nSkipForChargeInjectionOffset]
+for i in range(rawData.shape[2]):
+    data[:,:, i] = rawData[:,:, i] - pedestal
+print(data[:,:, 666].mean())
+
+data = data[:,:,nSkipForChargeInjectionOffset:]
+dataHighSignalPixel = dataHighSignalPixel[nSkipForChargeInjectionOffset:]
+dataHighDarkPixel = dataHighDarkPixel[nSkipForChargeInjectionOffset:]
+
+doCM = [True,False][1]
+
+plt.scatter(x[dataHighSignalPixel], data[signalPixel[0],signalPixel[1],:][dataHighSignalPixel],color='slateblue')
+plt.scatter(x[~ dataHighSignalPixel], data[signalPixel[0],signalPixel[1],:][~ dataHighSignalPixel], color='darkblue')
+
+## real photons are quantized, allowing cut to make sense even for signal pixels
+if doCM:
+    label += " column common mode correction"
+    for i in range(data.shape[2]):
+        data[:,:,i] = colCommonModeCorrection(data[:,:,i], 32000)
+else:
+    label += " no common mode correction"
+
+plt.scatter(x[dataHighDarkPixel], data[darkPixel[0],darkPixel[1],:][dataHighDarkPixel], color='orange')
+plt.scatter(x[~ dataHighDarkPixel], data[darkPixel[0],darkPixel[1],:][~ dataHighDarkPixel], color='goldenrod')
+plt.title("Alex data, %s" %(label))
+plt.xlabel("injection")
+title = "test pixels %d,%d, %d,%d in file %s" %(signalPixel[0], signalPixel[1], darkPixel[0], darkPixel[1], label)
+plt.savefig(title.replace(' ', '_'))
+plt.clf()
+
+
+##plt.hist(data.flatten().clip(0,40000), 100)
+plt.hist(data[data<gainCut].flatten(), 100)
+plt.hist((data[data>=gainCut].flatten()), 100, alpha=0.5)
+plt.title("Alex data, %s" %(label))
+plt.xlabel("ADU")
+title = "all pixels in file %s" %(label)
+##plt.savefig(title.replace(' ', '_'))

standalone_scripts/makePietroPixels.py

@@ -0,0 +1,24 @@
+import numpy as np
+roi = np.zeros([4, 168, 192])
+roi[0, 109:157, 0:48] = 1
+np.save("../data/epixUHR_asic0_sensor_fullRoi.npy", roi)
+roi = np.zeros([4, 168, 192])
+roi[3, 112:160, 10:58] = 1
+np.save("../data/epixUHR_asic3_sensor_fullRoi.npy", roi)
+roi = np.zeros([4, 168, 192])
+for r in range(109, 157):
+    for c in range(48):
+        if r%12 == 11 and c%6 == 0:
+            roi[0, r, c] = 1
+np.save("../data/epixUHR_asic0_sensor_pietroPixelRoi.npy", roi)
+for r in range(111, 160):
+    for c in range(10, 58):
+        if r%12 == 11 and c%6 == 0:
+            roi[3, r, c] = 1
+np.save("../data/epixUHR_asic3_sensor_pietroPixelRoi.npy", roi)
+roi = np.zeros([4, 168, 192])
+roi[3, 58:107, 70:119] = 1
+np.save("../data/epixUHR_asic3_offSensor_fullRoi.npy", roi)
+roi = np.zeros([4, 168, 192])
+roi[0, 11:59, 60:109] = 1
+np.save("../data/epixUHR_asic0_offSensor_fullRoi.npy", roi)

suite_scripts/LinearityPlotsParallelSlice.py

@@ -362,7 +362,10 @@ def analyze_h5_slice(self, dataFile, label):
         print("using flux label:", lpp.fluxLabel)
         lpp.fitInfo = None
         lpp.analyze_h5(lpp.file, lpp.label + "_raw")
-        lpp.analyze_h5_slice(lpp.file, lpp.label + "_raw")
+        ## modify for speed...
+        slow = True
+        if slow:
+            lpp.analyze_h5_slice(lpp.file, lpp.label + "_raw")
         print("done with standalone analysis of %s, exiting" % (lpp.file))
         logger.info("done with standalone analysis of %s, exiting" % (lpp.file))
         sys.exit(0)