From 3344236104281a84a729d2a7893481d4a3462f80 Mon Sep 17 00:00:00 2001 From: NiclasSvenMueller <84033855+NiclasSvenMueller@users.noreply.github.com> Date: Wed, 9 Mar 2022 16:04:34 +0000 Subject: [PATCH 1/2] Update Condense_DF_Spectra.py --- nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py b/nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py index fdc5aeb8..f772c409 100644 --- a/nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py +++ b/nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py @@ -415,10 +415,10 @@ def consoliData(rootDir): dTileNew = gTiles.create_dataset(tileName, data = dTileOld) dTileNew.attrs.update(dTileOld.attrs) - dReconTilesOld = ipf[scanName]['reconstructed_tiles'] - dReconTilesnew = consolidatedScan.create_dataset('reconstructed_tiles_%s' % scanN, - data = dReconTilesOld) - dReconTilesnew.attrs.update(dReconTilesOld.attrs) + #dReconTilesOld = ipf[scanName]['reconstructed_tiles'] + #dReconTilesnew = consolidatedScan.create_dataset('reconstructed_tiles_%s' % scanN, + # data = dReconTilesOld) + #dReconTilesnew.attrs.update(dReconTilesOld.attrs) existingParticles = sorted([i for i in consolidatedScan.keys() if i.startswith(gParticleFormat)], key = lambda i: int(i.split('_')[-1])) From be3b956fa5224386db7d1814518ee9776b3f48d9 Mon Sep 17 00:00:00 2001 From: NiclasSvenMueller <84033855+NiclasSvenMueller@users.noreply.github.com> Date: Wed, 9 Mar 2022 16:26:08 +0000 Subject: [PATCH 2/2] Update Condense_DF_Spectra.py missing background subtraction for reference DF spectrum (except for first iteration of loop when referenced = false) --- nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py b/nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py index f772c409..33fe9cba 100644 --- a/nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py +++ b/nplab/analysis/NPoM_DF_Analysis/Condense_DF_Spectra.py @@ -562,7 +562,9 @@ def extractAllSpectra(rootDir, returnIndividual = True, pl = False, dodgyThresho x = zScan.attrs['wavelengths'] bg = zScan.attrs['background'] ref = zScan.attrs['reference'] - + ref -= bg + ref = np.where(ref != 0, ref, 1) + except: print('Z-Stack not found in %s' % (groupName)) cancelled += 1