# -*- coding: utf-8 -*- """ Created on Mon May 28 16:48:33 2018 @author: Giovanni Galizia """ # all flags from IDL now as lists import pandas as pd import os def IDL_default_flags(STG_MotherOfAllFolders=''): # this version taken from master_jacob_sorted.pro # if STG_MotherOfAllFolders is empty, then current working directory is used #, sample master file #, containing all available flags as of september 2008 #, sorted in logical groups #, note, however, that not all flag settings are mentioned #, you still need to know what you can do and what the program does #, and you still need to run the necessary constrols # ALL IDL flags are in here now, # ALSO those that were not called flags # and the Movie flags also # however - all commented out. Only free those that are being used # in order to keep track of the new code if STG_MotherOfAllFolders == '': STG_MotherOfAllFolders = os.getcwd() IDL_flag = pd.Series({ ## system flags, many not necessary for the python version "VIEW_batchmode": 1, # choice between interactive mode and VIEW_batchmode # "MacSystem": "deprecated", ## format flags, not all necessary for python version # "TrueColour": 1, "SO_MV_colortable": 13, ## ##,***************************** ##,flags related to LOADING DATA ##,***************************** ## ## ,format of data files (used in LoadDataMaster.pro) "LE_loadExp" : 3, #20, # 3,4 , 0 for old setup, to 1 for Visicam, 2 for confocal ## ,TILL photonics single wavelength: 3 ## ,TILL photonics dual wavelength (FURA): 4 ## ,ZEISS multiphoton data: 20 ## ## ,should the raw data be median filtered? (used in ViewLoadData\MedianCorrection.pro) "Data_Median_Filter" : 0, #in ViewLoadData.MedianCorrection ## ,do a median correction when loading the data ## ,0: no median ## ,1: median in space fixed values ## ,2: median in time fixed values ## ,3: median in space and time, using flag values (Data_Median_Filter_space)(Data_Median_Filter_time) "Data_Median_Filter_space": 3, ## , used with Data_Median_Filter eq 3 "Data_Median_Filter_time": 0, ## , used with Data_Median_Filter eq 3 ## ## ,apply an off-line binning (shrinkFaktor). "LE_ShrinkFaktor": 0, # ,no shrinkfaktor with 1 ## ## ,are there different focal depth to be split? # "RM_separateLayers": 0, ## ,separates the layers in exportGlomeruli and SingleOverviews ## ## ,how to make movement correction based on .moveList file. (used in ViewLoadData\MovementCorrectionMaster.pro) "CSM_Movement": 0, ## ,set to 0: no movement correction (BUT shifts from .lst file are USED!) ## ,set to 1: on the spot movement correction ## ,set to 2: as 1, but calculated movements are saved in the moveList file ## ,set to 3: movement values are read from the moveList file ## ,set to 5: no movement correction, but shifts are taken from the movement file ## ,values above 10: mathiasCorrection. # "CSM_DataShift": 0, ## ,set to 0: data is NOT shifted, coordinates ARE shifted ## ,set to 1: data IS shifted, coordinate are NOT shifted ## ,set to 2: NONE is shifted ## ## ,trim the data frames to be loaded ## ,remove n frames at the beginning of each measurement # "CSM_SkipFrmUpFront": 0, ## ,remove n frames at the end of each measurement # "CSM_SkipFrmAtBack": 0, ## ## ,settings to reduce memory usage # "VIEW_No4Darray": 1, ## ,this reduces the sig1 array to a 3D array instead of a 4D array, not all routines work with this setting ## ,set to 1: odor 0 is cut off memory after loading the data, p1.odors is reduced by 1 #### Python: implement single odor use only, for now #### therefore VIEW_No4Darray is 1 by default #### sig1 is (x,y,t) and not (x,y,t,o) ## "VIEW_DeleteRawData": 0, ## ,this removes the raw data from memory after loading ## ## ,correct for scattered light, improving spatial resolution (used in CalcSigAll3000.pro) "VIEW_ScatterLightFactor": 0, ## ,for the 3xyy and 4xyy family with scattered light correction, this factor gives the strength of the unsharp mask. Default: 1 ## ,only used if (yy ne 00) ## ## ,load more than one experiment at the time # "view_MultiExp": 0, # , 0 for single experiment ## ,load AIR trial alongside the odor response (air trial is given in control column in the .lst file) "LE_AskForAir": 0, # , 0 for not loading air ## ##,END of flags related to loading data ## ## ##,************************************ ##,flags related to CALCULATING SIGNALS ##,************************************ ## ## ,how to calculate the data (used in ViewCalculateData\CalcSigMaster.pro) "LE_CalcMethod" : 4900, #see calcsigmaster3000 ## ,family 3xyy (deltaF/f) and 4xyy (ratio) uses x for bleach correction settings, and yy for scattered light correction ## ,see CalcSigAll3000.pro for detailed settings. Example are: ## , setting: 0 1 2 3 4 5 6 7 8 9 ## ,alPerimeter + + + + - - - - C - , with 8 bleaching is in coordinates only (variable: CoorPerimeter) ## ,excludeStim - + - + - + - + - - , exclude stimulus is obsolete - controled by LE_BleachStartFrame group ## ,addNoise - - + + - - + + - - ## ,no bleach - - - - - - - - - + ## ,air bleach - - - - - - - - + - ,correct with bleach parameters taken from air trial ## ,set to 3 for no calculation (original data). ## ## ,which frames to use for calculating F in deltaF/F "LE_StartBackground" : 4,# for deltaF/F calculations, or bleach corrections ## ,set to -1 not to subtract background in data calculation, to frame for background start. Default: 4 "LE_PrestimEndBackground" : 1, # for deltaF/F calculations, or bleach corrections ## ,How many frames before stimulus to stop with background. Default: 2 ## ,so: background is calculated from LE_StartBackground to StimulusOn - LE_PrestimEndBackground ## ,that means that StimulusOn is an important parameter and needs to be set correctly for deltaF/F ## ## ,settings for bleach correction when using CalcSigAll3000 "LE_BleachStartFrame" : 1, #start bleaching correction here ## ,for logarithmic bleach correction, all frames smaller are excluded in the fit function ## ,used in CalcSigAll3000, default 2 "LELog_InitialFactor" : 3, # weigh the frames before stimulus more than those after stimulus ## ,for logarithmic bleach correction, all frames before stimulus onset are more important by this factor ## ,used in CalcSigAll3000, default 1 for maximum compatibility "LELog_ExcludeSeconds" : 6, #how many seconds should be excluded during stimulation for bleach log fitting? ## ,for logarithmic bleach correction, how many seconds after stimulus onset to exclude ## ,used in CalcSigAll3000, default 0 for maximum compatibility ## ,this uses the time information - therefore make sure that is correct ## ,graphic display of weights can be switched of and on in the program CalcSigAll3000 # "LE_ClipPixels" : -2000, #how many seconds should be excluded during stimulation for bleach log fitting? ## ##,END of flags related to calculating signals ## ## ##,************************************ ##,flags related to SIGNAL CORRECTIONS ##,************************************ ##,note: this is for the extra set of corrected signals, not for corrections done during loading or calculation ## ## # "VIEW_InitCorr" : -1 ,# 18 : inverted (Fura at 810nm). set to -1 in order not to create a corrected data set # "VIEW_CorrSignals" : 0 ,# set to 1 to access corrected dataset, to 0 to access original data set ## ## ## ##,************************************* ##,flags related to data analysis OUTPUT ##,************************************* ## "VIEW_ReportMethod" : 10 , #which output do you want? This is one of the main flags ## , all settings are in View_gr_reports\subloop_report.pro, the most often used are ## , 10: false-color coded pictures (calls reportTIFF) ## , 11, 111: glodatamix (without, with tags) ## , 12: movies ## , 15: single TIFFs ## , 19: 119: glodatamix with CTV (without, with tags) ## "CTV_Method" : 22 , #curve-to-value function for single number output or still images ## , 22 gives ## , 22 is the difference between two fixed points ## , 35 relates to the maximum within 3 secs after stimulus onset ## , all values in ViewOverview\CurveToValue ## , values below 0 go to personal program in ImageALlocal folder: CurveToValueLocal.pro # "CTVM_Method" : 0,# , for multiple CTV values at once, not safely implemented yet ## ## "firstframe" was not in flags "CTV_firstframe" : 18 ,# many CTVs use fixed frames. These use the variables firstFrame and lastFrame "CTV_lastframe" : 22 , #for example, CTV 22 calculates the difference between lastframe (3 frames) and firstframe (3 frames) ## # "LE_FirstBuffer" : 1 , #sets which buffer to start with in output routines ## , standard is 1. Set to 0 to start with 0 (generally 0 is empty) ## , instead of LE_firstbuffer you can use LE_usefirstbuffer (synonymous) ## ## ,old flags, currently out of fashion # "PTA_PlotTimeRange" : 0,# # "PTA_PlotMeanValue" : 0,# ## ## ,flags specifically for graphical output (TIFF files and the like, i.e. "overviews") "SO_Method" : 10 , #used in ViewOverview\Overview.pro. Only values 0 or 10 are used now ## , 0 for calculations pixel by pixel (i.e. on the time-course in each pixel) ## , 10 for calculations frame by frame (much faster, but not all functions are possible) ## , for 10, the CTV value is applied within ViewOverview\overview10ctv.pro "SO_individualScale" : 0,# what scaling to use? 0 for fixed values, else individual scale for each frame ## , 3 for scaling within center of each frame ## , can be used in quite sophisticated ways, see ViewOverview\SingleOverviews.pro ## , also explained in the documentation ## "SO_MV_scalemax" was not in flags "SO_MV_scalemax": 18.000 ,# value to scale maximum to with SO_indiScale equals 0 "SO_MV_scalemin": -5.000 ,# corresponding value for minimum ## # "SO_morphoBackgr" : 0 , #Used to show an anatomical picture with an overlay of only the strongest POSITIVE responses # "SO_morphoBackgrNeg" : 0 , #Used to show an anatomical picture with an overlay of only the strongest NEGATIVE responses "SO_withinArea" : 1 , #False-color output limited to the mask in the .area file ## "CTV_scalebar" : 1 , #some output options allow to print out the color scalebar (SingleOverviews.pro) "RM_fotook" : 0 , #Overlay other information to overview output, (SingleOverviews.pro) ## , 1: puts squares in the coordinate positions (from .coor file) ## , 5: shows the perimeter of the .area file # "RM_differentViews" : 0 ,# Change view, e.g. mirror flip right ALs (SingleOverviews.pro) "RM_unsharpmask" : False , #Post-hoc filter on false-color images (SingleOverviews.pro) ## "RM_NewColumn" : 1 , #Start a new column in "tapeten" output (SingleOverviews.pro) ## , this flag is generally set in the gr_XXX file ## ## ,old flags # "RM_PlotTrace" : 0 ,# # "RM_PrintAscii" : 0 ,# # "RM_PrintLine" : 1 ,# "RM_ROItrace" : 0 ,# to select area file in exportglomeruli "RM_nextposition" : [0,0], #position of a frame in output canvas ## ## ## ,flags for filters "RM_Radius" : 5 , #For calculating traces (glodatamix), or for some spatial filters #used in CalcSigAll3000, also singleoverviews ## "Signal_FilterSpaceFlag" was not in flags "Signal_FilterSpaceFlag" : 1 , #If set to 1, the signal is calculated on the time trace at each pixel ## , after taking the mean of the pixels around it (RM_Radius). Therefor this is a slow filter ## , If set to 0, this filter is switched off "Signal_FilterSpaceSize" : 3 , #Filter size applied after overview calculation, always. ## , set to 0 when Signal_FilterSpaceFlag is on, to avoid double filtering. "Signal_FilterTimeFlag" : 1 , #Switch for the temporal filter "Signal_FilterTimeSize" : 3 ,# Size of the temporal filter ## ## ##,******************************************* ##,flags to control PATHS for input and output ##,******************************************* ## ## , this is one standard arrangement of folders ## , just adapt the STG_MotherOfAllFolders, but all subfolders must exist ## , place where all files are "STG_MotherOfAllFolders": STG_MotherOfAllFolders , # ## ## "STG_ReportTag" : 'animal' , #this contains the animal flag, set this for each round and animal, ( jacob: if not using the gr_xxx method) ## , this is set within the gr_file "STG_Measu" : 0, # measurement tag in .lst file [added in Python] ## ## , folder for the data files, STG_MotherOfAllFolders added below #### "STG_Datapath": STG_MotherOfAllFolders + 'data_jacob_LSM\' "STG_Datapath" : os.path.join(STG_MotherOfAllFolders, 'data'), ## , folder for the .inf files "STG_OdorInfoPath" : os.path.join(STG_MotherOfAllFolders, 'Lists'), ## , folder for the .coor and the .area file "STG_OdormaskPath" : os.path.join(STG_MotherOfAllFolders, 'Coor'), ## , folder for the all OUTPUT files "STG_OdorReportPath": os.path.join(STG_MotherOfAllFolders, 'IDLoutput'), ## , folder for the all OUTPUT files "STG_OdorReportFile": 'XYZ', ## , can be used for any text # "STG_Missing" : '999', ## ## ##,************************************ ##,flags used for MOVIE output ##,************************************ ## ##, in interactive mode, these flags are overwritten by the values in ##, imageALlocal\SetExportMovieFlags.pro ##, the variables are defined in view.pro ## "mv_exportFormat" : 'stack_tif' ,#'mpg4', #3 ,# 1 for TIFF (single files), 2 for PICT (premiere), 3 for MPEG, 4 for multilayer GIF, 5: multilayer TIF ## , 6 for uncompressed AVI (generally the best) # in python, mv_exportformat is not with numbers any more, but with strings "mv_realTime" : 1 ,# insert frames per second, 0 for no realTime, 24 for MPEG, 15 for GIF->QuickTime ## , AVI can work with any time, therefore 0 IS realTIME. In the other formats, additional frames are invented to create real time ## , if a negative number is given, that many frames are removed "mv_SpeedFactor" : 1 ,# for exportFormat 6, increase or decrease speed of movie "mv_reverseIt" : 0 , #turn it upside down "mv_rotateImage" : 0 ,# rotate only image, , 0 for no action, 2 for 180 degrees "mv_cutborder" : 0 ,# how many pixels to cut from each side (border, to hide filter artefacts) "mv_morphoThreshold" : 0 ,# substitutes lower range with morphological image to be taken from file "mv_withinArea" : 0 ,# limits output to within the mask in xxx.area "mv_sdSignificanceCut" : 0 ,# cuts everything below that significance level. Stimulus is included in calculation, ignored if below 0.1. ## , , Not implemented yet "mv_markStimulus" : 1 ,# marks stimulus application with a red box "mv_percentileScale" : False ,# scaling to a percentaje of noise. don´t use "mv_individualScale" : 2 ,# follows a similar logic to ("so_indiScale") ## ,0, 1: Pixmin and Pixmax are taken ## ,2 : min and maximum of sequence is taken ## ,3 : min and max of central region is taken ## ,4 : max of sequence is taken, min is Pixmin ## ,5 : min and max from area region ## ,6 : min from pixmin, max from area ## ,7 : min from pixmin, max from area but only stimulus + 2*stimulus length ## "mv_indiScale3factor" : 0.2 ,# set to 0.2 for 20 % border to be ignored when scaling usind idividualscale eq 3 ## , for mv_individualScale above 100 "mv_percentileValue" : 0 ,# : float(individualScale MOD 100)/100.0 "mv_xgap" : 50 ,# vertical + horizontal gaps, only even numbers! "mv_ygap" : 50 ,# 6, 10 "mv_correctStimulusOnset" : 0 ,# value to be added to stimulus onset (in frames) "mv_displayTime" : True ,# time in ss:ms as figures "mv_minimumBrightness" : 0 ,# creates a mask that depends on the brightnes of the foto "mv_suppressMilliseconds" : True, ## ## ## ,these flags are for interactive use in view (fasttraces) ## ,but are also used in movies to select a frame range for movie output ## ,set both to -1 to calculate the entire movie, else to fixed frame numbers "FT_FirstFrame" : -1 ,# show trace subsed in fast traces in VIEW "FT_LastFrame" : -1 ,# show trace subsed in fast traces in VIEW #the Ajay programs do not use FT_FirstFrame, but mv_FirstFrame, and more "mv_FirstFrame" : -1 ,# show trace subsed in fast traces in VIEW "mv_LastFrame" : -1 ,# show trace subsed in fast traces in VIEW "mv_bgColor" : 'b' , "mv_bitrate": '1024k', # values are 'single_tif', 'stack_tif', 'libx264' or other codecs "mv_fgColor": 'w' ## ## ,flags that are also relevant for movies, do NOT change them here to avoid confusion, change them above ## ,check program viewoverview\Exportmovie ## ,"ctv_scalebar" ## ,scaleMin ## ,scaleMax ## ,filterSpaceFlag ## ,filterSpaceSize ## ,SO_MV_colortable ## ,FILENAME defined in localOdorText ##,end of movie settings ## ## ## ##,************************************ ##,flags NOT USED for off-line analysis ##,************************************ ## ## "LE_ShowBox" : 0 , ## "FT_AllOdors" : 0 , show all odor traces in fast traces in VIEW ## "FT_TimeXAxis" : 0 , show time as x-axis in fast traces in VIEW ## "FT_Subset" : 0 , show trace subsed in fast traces in VIEW ## "FT_SelectFrame" : 0 , show trace subsed in fast traces in VIEW ## ## ##,"VIEW_InitCorr" : -1 , erase this line after analysis of these animals ##, "STG_OdorReportPath" : STG_MotherOfAllFolders + 'IDL_jacob_glomInteraction\IDLoutput\movies\j080730b\' ##,gr_takefromlist, 'j080730b',2 ##, "STG_OdorReportPath" : STG_MotherOfAllFolders + 'IDL_jacob_glomInteraction\IDLoutput\movies\j080730c\' ##,gr_takefromlist, 'j080730c',2 }) # here: change STG paths to add "mother of all directories" to it #test return IDL_flag ######################################################### ########## Main starts here ######################################################### #define flag structure IDL_flag = IDL_default_flags('') # can also be called with empty brackets() # end of program