Merge branch 'development' of github.com:slaclab/beamtime-calibration…

…-suite into development

calibrationSuite/basicSuiteScript.py

@@ -391,7 +391,7 @@ def addFakePhotons(self, frames, occupancy, E, width):
     def getNswitchedPixels(self, data, region=None):
         return (((data>=self.g0cut)*1).sum())
 
-
+"""
 if __name__ == "__main__":
     bSS = BasicSuiteScript()
     print("have built a BasicSuiteScript")
@@ -400,3 +400,4 @@ def getNswitchedPixels(self, data, region=None):
     evt = bSS.getEvt()
     print(dir(evt))
     logger.info(dir(evt))
+"""

docs/testing.md

@@ -32,8 +32,8 @@ These tests verify that the code in _/calibrationSuite_ and _/suite\_scripts_ is
 _test\_SuiteScripts.py_ runs the files in _/suite\_script_ and diffs their real output against expected output in _/tests/test\_data_  
 
 _/tests/test\_data_ stores data from this repo: <https://github.com/slaclab/beamtime-calibration-suite-test-data>
-The repo is added as a [git submodule](https://www.git-scm.com/book/en/v2/Git-Tools-Submodules), and should be setup by the _setup_developers.sh_ script.  
+The repo is added as a [git submodule](https://gist.github.com/gitaarik/8735255), and should be setup by the _setup_developers.sh_ script.  
 Since the test data is large, [LFS](https://docs.github.com/en/repositories/working-with-files/managing-large-files/installing-git-large-file-storage) is used and needs to be installed. (LFS is installed already on _S3DF_)  
 
 
-Some more info on testing, such as adding now data to the _test\_data_ submodule or add a new test-case to_suite\_scripts_ tests, can be found [in this file.](https://github.com/slaclab/beamtime-calibration-suite/blob/development/tests/test_SuiteScripts.py)
+Some more info on testing, such as adding now data to the _test\_data_ submodule or add a new test-case to_suite\_scripts_ tests, can be found [in this file.](https://github.com/slaclab/beamtime-calibration-suite/blob/development/tests/test_SuiteScripts.py)

suite_scripts/LinearityPlotsParallelSlice.py

@@ -168,7 +168,10 @@ def analyze_h5(self, dataFile, label):
         g0Fluxes = []
         g1s = []
         g1Fluxes = []
+
+        count = 0
         for s, _ in enumerate(self.singlePixels):
+            count += 1
             g0s.append(pixels[:, s, 1][pixels[:, s, 0] == 0])
             g0Fluxes.append(fluxes[pixels[:, s, 0] == 0])
             g1s.append(pixels[:, s, 1][pixels[:, s, 0] == 1])
@@ -203,7 +206,15 @@ def analyze_h5_slice(self, dataFile, label):
 
         for module in [1, 2]:
             for i in range(rows):
+                # so we can end early on testing runs:
+                if self.special is not None and 'testing' in self.special and i >= self.maxNevents:
+                    break
+
                 for j in range(cols):
+                    # so we can end early on testing runs:
+                    if self.special is not None and 'testing' in self.special and j >= self.maxNevents:
+                        break
+
                     iDet, jDet = self.sliceToDetector(i, j)
                     if False:
                         self.fitInfo[module, i, j, 8] = self.g0Ped[module, iDet, jDet]
@@ -275,10 +286,6 @@ def analyze_h5_slice(self, dataFile, label):
                                     plt.scatter(x, y - fitFunc, zorder=3, marker=".")
                                     plt.figure(1)
 
-<<<<<<< HEAD
-                    if i % 2 == 0 and i == j:
-                        figFileName = "%s/%s_slice_m%d_r%d_c%d_r%d_c%d_%s.png" % (self.outputDir, self.className, module, i, j, self.run, self.camera, label)
-=======
                 if i % 2 == 0 and i == j:
                     figFileName = "%s/%s_slice_%d_%d_r%d_c%d_%s.png" % (
                         self.outputDir,
@@ -303,10 +310,10 @@ def analyze_h5_slice(self, dataFile, label):
                             self.camera,
                             label,
                         )
->>>>>>> 7227771506c6eb7fcf01086cf40746763a0c61c1
                         plt.savefig(figFileName)
                         logger.info("Wrote file: " + figFileName)
                         plt.close()
+
                         if self.residuals:
                             plt.figure(2)
                             figFileName = "%s/%s_slice_m%d_r%d_c%d_r%d_c%d_residuals_%s.png" % (self.outputDir, self.className, module, i, j, self.run, self.camera, label)
@@ -454,21 +461,18 @@ def analyze_h5_slice(self, dataFile, label):
 
         smd.event(
             evt,
-<<<<<<< HEAD
-            eventDict
-=======
+            eventDict,
             fluxes=flux,
             rois=np.array(roiMeans),
             pixels=np.array(singlePixelData),
             slice=rawFrames[lpp.regionSlice],
->>>>>>> 7227771506c6eb7fcf01086cf40746763a0c61c1
         )
 
         nGoodEvents += 1
         if nGoodEvents % 100 == 0:
             print("n good events analyzed: %d" % (nGoodEvents))
             logger.info("n good events analyzed: %d" % (nGoodEvents))
-        ##            print("switched pixels: %d" %((switchedPixels>0).sum()))
+        ## print("switched pixels: %d" %((switchedPixels>0).sum()))
 
         if nGoodEvents > lpp.maxNevents:
             break

tests/test_SuiteScripts.py

@@ -282,7 +282,8 @@ def test_SinglePhoton(suite_tester, command, output_dir_name):
             [
                 "bash",
                 "-c",
-                "python LinearityPlotsParallelSlice.py -r 102 --maxNevents 250 -p /test_linearity_scan -f test_linearity_scan/LinearityPlotsParallel__c0_r102_n666.h5 --label fooBar",
+                # this cmd runs pretty long, so we use '--special testing' and '-maxNevents 2' to stop pixel-analysis early
+                "python LinearityPlotsParallelSlice.py -r 102 --special testing --maxNevents 2 -p /test_linearity_scan -f test_linearity_scan/LinearityPlotsParallel__c0_r102_n666.h5 --label fooBar",
             ],
             "test_linearity_scan",
         ),