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GetParams.m
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function params=GetParams(paramSet,isOnCluster,varargin)
if(nargin<2)
isOnCluster=false;
end
if(isOnCluster)
zDrive='/awlab/users/srajaram/';
else
zDrive='/home/z/';
end
params=struct;
switch(paramSet)
case 'Papadeno'
params.tmaRadius=650; % comes from 0.6mm diameter core with ~ 0.4626 microns per pixel imaging.
params.dataDir=fullfile(zDrive,'Data/Papadeno_Aperio');
params.afiFile=fullfile(params.dataDir,'Papadeno_L34_MS1_Tumor3_2Channel.afi');
%params.afiFile=fullfile(params.dataDir,'Papadeno_L34_MS1_Tumor3.afi');
%params.channelNames={'DAPI','Ki67','TTF1','Bad'};
params.channelNames={'DAPI','TTF1'};
params.tumorOutlineFilename=fullfile(params.dataDir,'Papadeno_L34_MS1_Tumor3_TumorArea.xml');
params.masksAndCoresFile=fullfile(params.dataDir,'cluster_nuclear1_Papadeno_L34_MS1_Tumor3_1.mat');
params.pp_cutoff=10000;
params.displayed_core_centers=8*[1421 705;1777 2235];
case 'LiverCancer'
% TMA Core Properties
params.tmaRadius=300; %TMA radius in microns (300 corresponds to 0.6mm diameter cores)
params.minCoreFgFraction=0.7; % Fraction of Core that must be cellular for core to be used
% p=inputParser;
% acceptableMaskTypes={'Auto','JG'};
% addparameter(p,'MaskType','JG',...
% @(x) validatestring(x,acceptableMaskTypes));
%
% parse(p,varargin{:});
%
% params.maskType=p.Results.MaskType;
params.maskType='Auto';'JG'; % Auto means only badly stained regions (identified automatically) will be dropped, whereas JG uses masks of
% tissue regions drawn by John Gordan
%Image Data Paths
params.yapLkb1ImgDir=fullfile(zDrive,...
'/Data/JG_images/AxioScan_June2016/Tiffs/');
params.yapBcatVersaImgDir=fullfile(zDrive,...
'/Data/JG_images/Versa_April2016/');
params.yapBcatAxioImgDir=fullfile(zDrive,...
'/Data/JG_images/Axio_Bcat/');
switch(params.maskType)
case 'JG'
params.masksDir=fullfile(zDrive,...
'/Data/JG_images/Masks/JG/');
params.coreCoordsDir=fullfile(zDrive,...
'/Data/JG_images/CoreCoords/JG/');
case 'Auto'
params.masksDir=fullfile(zDrive,...
'/Data/JG_images/Masks/Auto/');
params.coreCoordsDir=fullfile(zDrive,...
'/Data/JG_images/CoreCoords/Auto/');
end
% Annotation
params.clinicalInfoFileName=fullfile(zDrive,...
'/Data/JG_images/160623 HCC specimen clinical info for Satwik.xlsx');
params.pathInfoFileName=fullfile(zDrive,'/Data/JG_images/HCC specimen path comments 11-10-15.xlsx');
params.mappingFile=fullfile(zDrive,'/Data/JG_images/Img2sample_alt.mat');
if(isOnCluster)
params.sampleAnnotationFile=fullfile(zDrive,...
'/Data/JG_images/SampleAnnotationCluster.mat');
else
params.sampleAnnotationFile=fullfile(zDrive,...
'/Data/JG_images/SampleAnnotation.mat');
end
%Results Paths
params.segResDir=fullfile(zDrive,...
'Cluster/Tissue_Length_Scale/Nuclear_Segmentation/Results/');
switch(params.maskType)
case 'JG'
params.kspResDir=fullfile(zDrive,...
'Cluster/Tissue_Length_Scale/KSP_Calculation/Results/JG/');
case 'Auto'
params.kspResDir=fullfile(zDrive,...
'Cluster/Tissue_Length_Scale/KSP_Calculation/Results/Auto/');
end
case 'CellCulture'
params.kspResultFile='/home/srajaram/Work/Tissue/Code/tissue_length_scale/Cell_Culture/Well_Variation_Results.mat';
params.plateDataDir='/home/project/2015_09_HTS_LE/2016/';
params.plateDataDir='/home/project/2015_09_HTS_LE/plates/2016/';
params.altPlateDataDir='/home/project/2015_09_HTS_LE/plates/2016/';
params.plateList={'LE_20160202_InCell_plate_2016018019_10x_t24',...
'LE_20160202_InCell_plate_2016018020_10x_t24',...
'LE_20160202_InCell_plate_2016018021_10x_t24',...
'LE_20160202_InCell_plate_2016018022_10x_t24',...
'LE_20160202_InCell_plate_2016018023_10x_t24',...
'LE_20160202_InCell_plate_2016018024_10x_t24',...
'LE_20160202_InCell_plate_2016018025_10x_t24'};
otherwise
error('Unrecognized Parameter Set');
end
end