pyview_test_data/AS_Till_2004/IDL_Progs/PNs_gcamp.pro

pro PNs_gcamp

common data
common vars
common CFD
common CFDconst


;tiff:        0,45,2,10,17,21,2,1,7
;on raw data: 0,45,2,10,15,240,2,1,7,5 does not work yet
;coordinates: 0,45,2,9,17,21,4,1,7,4
;New TIFFs :  1,45,2,10,21,33,4,1,7,4,0
;New coordinates: 1,45,2,9,21,21,4,1,7,4
;export glomeruli time courses: 0,45,2,11,15,x,4,0,7,0,x,x

;IN COMMON VARS
colortable  = 39;0;43;41  ;45 for TIFF output, 0 for black/white; 37 for blue_black_red_white; 38 for black_red_white
;set flags here
;loading the data and calculate signals
flag[view_loadExp]      = 3;3;4 	; 0 for old setup, to 1 for Visicam, 2 for confocal
flag[view_CalcMethod]   = 3500; 3550: bleachcorrect,excludstim
							;3150: bleachcorrect,excludstim,withinAl
							;3750: bleachcorrect, excludestim, addnoise
							;4950; 3 (original data); 10 for fura ; for bleaching is incluiding in 9 and 10 ;***** normalerweise 7 oder 8, schnelle Berechnung 0
flag[csm_median]        = 0; !!!!!!!!!!!!!!!change!!!!!!!   0: no correction, 1: median in space fixed values, 2: space and time fixed values; 3: space and time, using flag values
	flag(csm_median_space)= 3
	flag(csm_median_time) = 0
flag[csm_movement]      = 0; movement correction; 3: to include the movcorr from mathias´ program
flag[CSM_DataShift]		= 1 ; shift data instead of mask
flag[le_shrinkFaktor]	   = 1     ;no shrinkfaktor with 1
flag[RM_separateLayers] = 0 ;separates the layers in exportGlomeruli and SingleOverviews


;view the data analysis
flag[view_reportMethod] =1003;1003: for mathias´program; 11;10;-1 	; check in subloop.pro
						; 10: TIFF-Ausgabe, 11: Traces-Berechnung, 12 : Movie; 13 : stack of tiff files; 19:CTV + Glodatamix; 14: .RAW; 15: single tiff files
firstframe = 1   ;for movie output
lastframe  = 4
;spacefilter: ft_radius wird nur benutzt, wenn FilterSpaceFlag gesetzt ist
;der zusätzliche SpaceFilter wird nur ausgeführt, wenn er gt 2 ist.
flag[ft_radius]   =3 ; setting 5 gives ca 25microns squares with 20x Obj in traces calculation
FilterSpaceFlag = 0 ;***** normalerweise 1, schnelle Berechnung 0
FilterSpaceSize = 0;***** normalerweise 2, schnelle Berechnung 0
FilterTimeFlag  = 0
FilterTimeSize  = 0
flag[so_indiScale]      = 0;7;1500;1101; 3     ; ShowOverviews : 0:scale according to values in control window
				;		  1 = scale each overviewframe to its own min/max
				;		  2 = scale to min/max of all
				;		  3 to central region of individual frame
				;		  5 to selected area of individual frame
				;		  2x scales both neg and positive with the same dynamics
				; setting also affects scaling in the movie output, see exprotmovie.pro
				; 7 in export movie: bottom fixed, top in area region
scalemax = 3.000
scalemin = -1.0
flag[rm_fotoOK]         =0;1;1;5   ; draw coordinate positions in TIFF output as white squares
flag[so_method]         = 0	; ShowOverviews Method: 1: mittleres Signal wŠhren Stimulus
								;0 for selecting CTV_method in the file CurveToValue.pro in ShowOverviews folder
								;10 for selecting CTV_method in the file Overview10ctv.pro in ShowOverviews folder
								;11 for correlation
flag[RM_differentViews] = 0     ;mirrors right ALs following the name in the list
flag[LE_UseFirstBuffer] = 1;0;
flag[so_morphoBackgr] = 0;150;150
flag[so_morphoBackgrNeg]= 0;95;105
flag[so_withinMask] =0
flag[CTV_scalebar] = 0
flag[LE_StartBackground] = 4; frame where background calculation starts (in general startbackground:stim_on frames are used for background calculation)
flag[LE_PrestimEndBackground] = 0 ;How many frames before stimulus to stop with background. Default: 2
flag[RM_ROITrace] =0
flag[VIEW_ScatterLightFactor] = 1;for the 3xxx and 4xxx family with scattered light correction, this factor gives the strength of the unsharp mask. Default: 1

; no change flags
CorrectFlag = 0;1;0              ;0:unkorrigiert, 1:luftkorrigiert
flag[macSystem]  = 0
flag[view_initCorr]     = -1;3;-1;1050;21;21;17 	; initial correction when loading data, -1 (= 15) for no correction at all (save memory)
flag[batchMode]         = 1
flag[le_AskForAir]	    = 0;1;0
flag[trueColour]        = 1
flag[rm_plotTrace]      = 0;1 	; reportMask, plots traces to screen when set
flag[rm_printAscii]     = 0 	; ReportMask,
flag[rm_PrintLine]      = 1 	; ReportMask
flag[view_MultiExp]     = 0 	; 0 for single experiment
flag[pta_plottimerange] = 0 	; PlotTraceArray if set, takes range from control window
flag[pta_plotMeanValue] = 0 	; PlotTraceArray





;pfade für Clementina
auswertungMother = 'K:\PNs\'
DatenMother      = 'K:\PNs\data\'


;path settings for all measurements
;location of the coordinate files
flag[stg_OdorMaskPath]    = auswertungMother+ 'IDLcoors\'            ;woher kommt die Maske ?
;path for the .lst files
flag[stg_OdorInfoPath]    = auswertungMother+ 'IDLlisten\'



;ReportPath, place for the IDL output
;flag[stg_OdorReportPath]  = auswertungMother+ 'IDLoutput\' ;wohin soll die Ausgabe ? und pharma (ttx, ptx, etc)

flag[stg_OdorReportPath]  = auswertungMother+ '\IDLoutput\' ;for concentration exps
;flag[stg_OdorReportPath]  = 'H:\ana\analysis_LNs\IDLoutput\'; in external hard disk
;flag[stg_OdorReportPath]  = auswertungMother+ 'synII\IDLoutput\' ;for concentration exps
longMeasurements           = 1
shortMeasurements          = 0

;one block for each animal follows, with specic settings


IF longMeasurements THEN begin

	flag[CTV_method] = -222;-12;-379;50;21;100;21			;22: take 3 frames aroung lastframe - 3 frames around firstframe
	firstframe = 7   ;for movie output
	lastframe  = 13

average_flag = 0 ; set to 0 for single measurements, 1 for averages, 2 for both





PNs_measu_gcamp, DatenMother ;, average_flag




endIF ;longMeasurements




IF shortMeasurements THEN begin

flag[view_CalcMethod]   = 12554; 5 (original data); 10 for fura ; for bleaching is incluiding in 9 and 10 ;***** normalerweise 7 oder 8, schnelle Berechnung 0
firstframe = 1   ;for movie output
lastframe  = 4
flag[CTV_method] = 22;50;21;100;21			;22: take 3 frames aroung lastframe - 3 frames around firstframe


;flag[CTV_method] = 300;50;21;100;21			;22: take 3 frames aroung lastframe - 3 frames around firstframe
;colortable  = 0
;CorrectFlag = 1




endIF ;shortMeasurements



end