BUG: make suite_scripts work with new psanabase class structure

calibrationSuite/psanaBase.py

@@ -41,6 +41,26 @@ def __init__(self, analysisType="scan"):
         print("in PsanaBase")
         logger.info("in PsanaBase")
 
+        # psana 1 + 2
+        self.ds = None
+        self.det = None
+        self.wave8 = None
+        self.evrs = None
+        self.config = None
+        self.controlData = None
+
+        # psana 2
+        self.myrun = None
+        self.step_value = None
+        self.step_docstring = None
+        self.timing = None
+        self.desiredCodes = None
+        self.mfxDg1 = None
+        self.mfxDg2 = None
+        self.detEvts = None
+        self.flux = None
+
+
     def setupPsana(self): 
         if psanaBaseNum == 2:
             setupPsana2(self)

calibrationSuite/suiteBase.py

@@ -443,7 +443,7 @@ def dumpEventCodeStatistics(self):
             % (self.nRunCodeEvents, self.nDaqCodeEvents, self.nBeamCodeEvents)
         )
 
-    def sortArrayByList(a, data):
+    def sortArrayByList(self, a, data):
         return [x for _, x in sorted(zip(a, data), key=lambda pair: pair[0])]
 
 

suite_scripts/CalcNoiseAndMean.py

@@ -7,9 +7,11 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 from calibrationSuite.Stats import *
 import calibrationSuite.loggingSetup as ls
+import os
+import numpy as np
 
 # for logging from current file
 logger = logging.getLogger(__name__)
@@ -18,10 +20,10 @@
 ls.setupScriptLogging("../logs/" + currFileName[:-3] + ".log", logging.INFO)  # change to logging.INFO for full logging output
 
 
-class CalcNoise(BasicSuiteScript):
+class CalcNoise(PsanaBase):
     def __init__(self):
         super().__init__("dark")
-
+        self.className = self.__class__.__name__
 
 if __name__ == "__main__":
     cn = CalcNoise()
@@ -83,6 +85,7 @@ def __init__(self):
                 print("no frame")
                 logger.info("no frame")
                 continue
+            print(statsArray)
             for i, p in enumerate(cn.singlePixels):
                 try:
                     statsArray[i].accumulate(np.double(frames), frames[tuple(p)])

suite_scripts/DeltaTtest.py

@@ -7,10 +7,10 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 
 
-class EventScanParallel(BasicSuiteScript):
+class EventScanParallel(PsanaBase):
     def __init__(self):
         super().__init__("misc")  ##self)
         self.only281 = [True, False][0]
@@ -144,7 +144,7 @@ def analyze_h5(self, dataFile, label):
 
     esp.setupPsana()
 
-    smd = esp.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (esp.outputDir, esp.className, esp.camera, esp.run, size))
+    smd = esp.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (esp.outputDir, esp.className, esp.camera, esp.run, esp.size))
 
     esp.fluxTS = 0
     esp.nGoodEvents = 0

suite_scripts/EventScanParallelSlice.py

@@ -7,7 +7,7 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 import calibrationSuite.loggingSetup as ls
 import logging
 import h5py
@@ -19,7 +19,7 @@
 currFileName = os.path.basename(__file__)
 ls.setupScriptLogging("../logs/" + currFileName[:-3] + ".log", logging.ERROR)  # change to logging.INFO for full logging output
 
-class EventScanParallel(BasicSuiteScript):
+class EventScanParallel(PsanaBase):
     def __init__(self):
         super().__init__("misc")  ##self)
         logging.info("Output dir: " + self.outputDir)
@@ -197,7 +197,7 @@ def analyze_h5(self, dataFile, label):
     except:
         skip_283_check = False ## for running at MFX
 
-    h5FileName = "%s/%s_c%d_r%d_n%d.h5" % (esp.outputDir, esp.className, esp.camera, esp.run, size)
+    h5FileName = "%s/%s_c%d_r%d_n%d.h5" % (esp.outputDir, esp.className, esp.camera, esp.run, esp.size)
     smd = esp.ds.smalldata(filename=h5FileName)
 
     esp.nGoodEvents = 0

suite_scripts/LinearityPlotsParallelSlice.py

@@ -7,7 +7,7 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import *
 import calibrationSuite.fitFunctions as fitFunctions
 import calibrationSuite.ancillaryMethods as ancillaryMethods
 
@@ -24,10 +24,12 @@
 ## ditto with 1
 
 
-class LinearityPlotsParallel(BasicSuiteScript):
+class LinearityPlotsParallel(PsanaBase):
     def __init__(self):
         super().__init__("scan")  ##self)
-        self.saturated = [True, False][1]
+        self.className = self.__class__.__name__
+
+        self.saturated = [True, False][0]
         print("using saturation fit =", self.saturated)
         logger.info("using saturation fit =" + str(self.saturated))
         self.residuals = [True, False][0]
@@ -291,7 +293,7 @@ def analyze_h5_slice(self, dataFile, label):
         logger.info("not doing Kaz events")
 
     lpp.setupPsana()
-    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))
+    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, lpp.size))
 
     nGoodEvents = 0
     fluxes = []  ## common for all ROIs

suite_scripts/PersistenceCheckParallel.py

@@ -7,13 +7,13 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 import sys
 import numpy as np
 import matplotlib.pyplot as plt
 
 
-class PersistenceCheckParallel(BasicSuiteScript):
+class PersistenceCheckParallel(PsanaBase):
     def __init__(self):
         super().__init__()  ##self)
         print("in", sys.argv[0])
@@ -57,7 +57,7 @@ def analyze_h5(self, dataFile, label):
         sys.exit(0)
 
     pc.setupPsana()
-    smd = pcp.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (pcp.outputDir, pcp.className, pcp.camera, pcp.run, size))
+    smd = pcp.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (pcp.outputDir, pcp.className, pcp.camera, pcp.run, pc.size))
 
     nEvent = -1
     nGoodEvents = 0

suite_scripts/SimpleClustersParallelSlice.py

@@ -7,11 +7,11 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 from calibrationSuite.cluster import Cluster, BuildClusters
 
 
-class SimpleClusters(BasicSuiteScript):
+class SimpleClusters(PsanaBase):
     def __init__(self):
         super().__init__("lowFlux")  ##self)
 
@@ -125,7 +125,7 @@ def analyze_h5(self, dataFile, label):
         sys.exit(0)
 
     sic.setupPsana()
-    smd = sic.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (sic.outputDir, sic.className, sic.camera, sic.run, size))
+    smd = sic.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (sic.outputDir, sic.className, sic.camera, sic.run, sic.size))
 
     ## 50x50 pixels, 3x3 clusters, 10% occ., 2 sensors
     maxClusters = 1000##int(50 * 50 / 3 / 3 * 0.1 * 2)

suite_scripts/analyze_npy.py

@@ -7,10 +7,12 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
+from calibrationSuite.psanaBase import PsanaBase
 import matplotlib.pyplot as plt
 import numpy as np
 import sys, re
-
+import logging
+import os
 from runInfo import *
 
 import calibrationSuite.loggingSetup as ls
@@ -21,7 +23,7 @@
 ls.setupScriptLogging("../logs/" + currFileName[:-3] + ".log", logging.INFO)  # change to logging.INFO for full logging output
 
 
-class LinearityInfo(object):  ## describes the .npy array
+class LinearityInfo(PsanaBase):  ## describes the .npy array
     def __init__(self):
         self.dataIndices = {
             "g0slope": 0,

suite_scripts/deprecatedLinearityPlotsParallel.py

@@ -7,15 +7,15 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 
 ## This builds and analyzes a dict with keys:
 ## 'rois' - ROI fluxes and means
 ## 'g0s' -per-pixel g0 fluxes and values, ragged or None-filled
 ## ditto with 1
 
 
-class LinearityPlotsParallel(BasicSuiteScript):
+class LinearityPlotsParallel(PsanaBase):
     def __init__(self):
         super().__init__("scan")  ##self)
 
@@ -141,7 +141,7 @@ def analyze_h5(self, dataFile, label):
         print("not doing Kaz events")
 
     lpp.setupPsana()
-    smd = lpp.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (lpp.outputDir, lpp.className, lpp.camera, lpp.run, size))
+    smd = lpp.ds.smalldata(filename="%s/%s_c%d_r%d_n%d.h5" % (lpp.outputDir, lpp.className, lpp.camera, lpp.run, lpp.size))
 
     ##    efs.setROI('roiFromSwitched_e398_rmfxx1005021.npy')
     if lpp.run >= 550 and lpp.run < 590:  ## pinhole study range

suite_scripts/findMinSwitchValue.py

@@ -7,10 +7,10 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 
 
-class FindMinSwitchValue(BasicSuiteScript):
+class FindMinSwitchValue(PsanaBase):
     def __init__(self):
         super().__init__()  ##self)
 

suite_scripts/histogramFluxEtc.py

@@ -7,10 +7,10 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 
 
-class HistogramFluxEtc(BasicSuiteScript):
+class HistogramFluxEtc(PsanaBase):
     def __init__(self):
         super().__init__()  ##self)
 

suite_scripts/persistenceCheck.py

@@ -7,13 +7,13 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 import sys
 import numpy as np
 import matplotlib.pyplot as plt
 
 
-class PersistenceCheck(BasicSuiteScript):
+class PersistenceCheck(PsanaBase):
     def __init__(self):
         super().__init__()  ##self)
         print("in", sys.argv[0])

suite_scripts/roiFromSwitched.py

@@ -7,10 +7,10 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 
 
-class RoiFromSwitched(BasicSuiteScript):
+class RoiFromSwitched(PsanaBase):
     def __init__(self):
         super().__init__()  ##self)
 

suite_scripts/roiFromThreshold.py

@@ -7,7 +7,7 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 
 
 class RoiFromThreshold(BasicSuiteScript):

suite_scripts/searchForNonSwitching.py

@@ -7,7 +7,7 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 
 
 class LinearityPlotsAutoranging(BasicSuiteScript):

suite_scripts/simplePhotonCounter.py

@@ -7,7 +7,7 @@
 ## may be copied, modified, propagated, or distributed except according to
 ## the terms contained in the LICENSE.txt file.
 ##############################################################################
-from calibrationSuite.basicSuiteScript import *
+from calibrationSuite.psanaBase import PsanaBase
 
 import calibrationSuite.loggingSetup as ls
 # for logging from current file
@@ -16,7 +16,7 @@
 currFileName = os.path.basename(__file__)
 ls.setupScriptLogging("../logs/" + currFileName[:-3] + ".log", logging.INFO)  # change to logging.INFO for full logging output
 
-class SimplePhotonCounter(BasicSuiteScript):
+class SimplePhotonCounter(PsanaBase):
     def __init__(self):
         super().__init__(analysisType="lowFlux")