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Kafri-Lab · Jul 3, 2017 · 9e63d2d · 9e63d2d
1 parent 1eac530
commit 9e63d2d
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Showing 4 changed files with 9 additions and 9 deletions.
diff --git a/islet_functions/LoadImages.m b/islet_functions/LoadImages.m
@@ -1,5 +1,5 @@
 function [DAPI, ECad, PDX1] = LoadImages(folder)
-  if or(contains(folder, '2nd image set'), contains(folder, '3rd image set'))
+  if strfind(folder, '2nd image set') | strfind(folder, '3rd image set')
     DAPI = im3dread(folder, '*.tif', 1); % channel: DAPI
     ECad = im3dread(folder, '*.tif', 2); % channel: e-cadherin
     PDX1 = im3dread(folder, '*.tif', 3); % channel: pdx1

diff --git a/islet_functions/NewMeasurements.m b/islet_functions/NewMeasurements.m
@@ -115,11 +115,12 @@
   newResults.Stack = stack_name';
 
   % EXPERIMANTAL CLASS (control, torin, or torin wash)
-  if or(contains(char(folder),'\ctl'),contains(char(folder),'\Control'))
+  if or(strfind(char(folder),'\ctl'), strfind(char(folder),'\Control'))
+  if strfind(char(folder), '2nd image set')
     experimental_class = 'Control'
-  elseif contains(char(folder),'\Torin_wash')
+  elseif strfind(char(folder),'\Torin_wash')
     experimental_class = 'Wash'
-  elseif contains(char(folder),'\Torin')
+  elseif strfind(char(folder),'\Torin')
     experimental_class = 'Torin'
   else
     error('Error: did not recognized folder: %s', folder)

diff --git a/islet_functions/SmoothIslet.m b/islet_functions/SmoothIslet.m
@@ -1,7 +1,7 @@
 function cyto_smooth = SmoothIslet(cyto, folder)
-  if contains(folder, '3rd image set')
+  if strfind(char(folder), '3rd image set')
     cyto_smooth = imgaussfilt3(cyto,[4 4 3]);
-  elseif contains(folder, '2nd image set')
+  elseif strfind(char(folder), '2nd image set')
       cyto_smooth = imgaussfilt(cyto,6);
   else
     error('Error: did not recognized folder: %s', folder)

diff --git a/islet_segmentation_pipeline.m b/islet_segmentation_pipeline.m
@@ -1,5 +1,4 @@
 set(0,'DefaultFigureWindowStyle','docked')
-addpath '\\carbon.research.sickkids.ca\rkafri\Miriam\Matlab function library'
 addpath '\\carbon.research.sickkids.ca\rkafri\YuvalDor\mouse islet z-stacks\code\islet_functions'
 inpath = '\\carbon.research.sickkids.ca\rkafri\YuvalDor\mouse islet z-stacks\images\';
 
@@ -25,9 +24,9 @@
 % '2nd image set\Whole_mount_cy5pdx_cy3E-cad_DAPI_140217\Torin_1-0004\Torin_1-0004\' ...
 % '2nd image set\Whole_mount_cy5pdx_cy3E-cad_DAPI_140217\Torin_1-0005\Torin_1-0005\' ...
 % '2nd image set\Whole_mount_cy5pdx_cy3E-cad_DAPI_140217\Torin_wash_1-0001\Torin_wash_1-0001\' ...
- '2nd image set\Whole_mount_cy5pdx_cy3E-cad_DAPI_140217\Torin_wash_1-0002\Torin_wash_1-0002\' ...
+ % '2nd image set\Whole_mount_cy5pdx_cy3E-cad_DAPI_140217\Torin_wash_1-0002\Torin_wash_1-0002\' ...
 % '2nd image set\Whole_mount_cy5pdx_cy3E-cad_DAPI_140217\Torin_wash_1-0003\Torin_wash_1-0003\' ...
-% '2nd image set\Whole_mount_cy5pdx_cy3E-cad_DAPI_140217\Torin_wash_1-0005\Torin_wash_1-0005\' ...
+'2nd image set\Whole_mount_cy5pdx_cy3E-cad_DAPI_140217\Torin_wash_1-0005\Torin_wash_1-0005\' ...
 };
 
 %% REJECTED ISLETS