Added specific entry points for Patrick pipeline

Author: adamltaylor

compute_landmarks.sh

@@ -0,0 +1,5 @@
+#! /bin/bash
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+cd "$SCRIPT_DIR"
+/misc/local/matlab-2019a/bin/matlab -batch "modpath; compute_landmarks_for_patrick_pipeline('$1', '$2', '$3')"

compute_landmarks_for_patrick_pipeline.m

@@ -0,0 +1,56 @@
+function compute_landmarks_for_patrick_pipeline(p_map_root_path, landmarks_root_path, tile_relative_path, ...
+                                                do_force_computation, do_run_in_debug_mode)                                    
+    % Deal with args
+    if ~exist('do_force_computation', 'var') || isempty(do_force_computation) ,
+        do_force_computation = false ;
+    end
+    if ~exist('do_run_in_debug_mode', 'var') || isempty(do_run_in_debug_mode) ,
+        do_run_in_debug_mode = false ;
+    end
+    
+    % Make sure the output folder exists
+    landmark_folder_path = fullfile(landmarks_root_path, tile_relative_path) ;
+    ensure_folder_exists(landmark_folder_path) ;
+    
+    % Run for all channels
+    channel_count = 2 ;
+    for channel_index = 1 : channel_count ,
+        compute_landmarks_for_single_tile_channels(p_map_root_path, tile_relative_path, landmarks_root_path, ...
+                                                   channel_index, ...
+                                                   do_force_computation, do_run_in_debug_mode) ;
+    end
+end
+
+
+
+function compute_landmarks_for_single_tile_channels(p_map_root_path, landmarks_root_path, tile_relative_path, ...
+                                                    channel_index, ...
+                                                    do_force_computation, do_run_in_debug_mode)
+                                                
+    % Compute the p-map file path    
+    [~,day_tile_index_as_string] = fileparts2(tile_relative_path) ;
+    channel_index0 = channel_index - 1 ; 
+    channel_index0_as_string = num2str(channel_index0) ;
+    p_map_file_name = sprintf('%s-prob.%s.h5', day_tile_index_as_string, channel_index0_as_string) ;
+    p_map_tile_folder_path = fullfile(p_map_root_path, tile_relative_path) ;
+    p_map_file_path = fullfile(p_map_tile_folder_path, p_map_file_name) ;
+    
+    % Generate the landmarks from the p-map
+    landmark_file_name = sprintf('%s-desc.%s.txt', day_tile_index_as_string, channel_index0_as_string) ;
+    landmark_folder_path = fullfile(landmarks_root_path, tile_relative_path) ;
+    landmark_file_path = fullfile(landmark_folder_path, landmark_file_name) ;
+
+%     % Make sure the output folder exists
+%     ensure_folder_exists(landmark_folder_path) ;
+    
+    % Run the core code
+    siz = '[11 11 11]' ;
+    sig1 = '[3.405500 3.405500 3.405500]' ;
+    sig2 = '[4.049845 4.049845 4.049845]' ;
+    ROI = '[5 1019 5 1531 5 250]' ;
+    rt = '4' ;    
+    exitcode = dogDescriptor(p_map_file_path, landmark_file_path, siz, sig1, sig2, ROI, rt) ;
+    if exitcode ~= 0 ,
+        error('dogDescriptor() returned a nonzero exit code (%s) when trying to produce output file %s', exitcode, landmark_file_path) ;
+    end
+end

compute_z_matches.sh

@@ -0,0 +1,5 @@
+#! /bin/bash
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
+cd "$SCRIPT_DIR"
+/misc/local/matlab-2019a/bin/matlab -batch "modpath; compute_z_matches_for_patrick_pipeline('$1', '$2', '$3', '$4', '$5')"

compute_z_matches_for_patrick_pipeline.m

@@ -0,0 +1,17 @@
+function compute_z_matches_for_patrick_pipeline(landmarks_root_path, z_matches_root_path, tile_relative_path, ...
+                                                fluorescence_root_path, other_tile_relative_path)                                        
+                                            
+    % Synthesize all the tile folder paths
+    central_tile_landmark_folder_path = fullfile(landmarks_root_path, tile_relative_path) ;
+    other_tile_landmark_folder_path = fullfile(landmarks_root_path, other_tile_relative_path) ;
+    central_tile_fluorescence_folder_path = fullfile(fluorescence_root_path, tile_relative_path) ;
+    other_tile_fluorescence_folder_path = fullfile(fluorescence_root_path, other_tile_relative_path) ;
+    output_folder_name = fullfile(z_matches_root_path, tile_relative_path) ;
+    
+    % Run for all channels
+    pointmatch(central_tile_landmark_folder_path, ...
+               other_tile_landmark_folder_path, ...
+               central_tile_fluorescence_folder_path, ...
+               other_tile_fluorescence_folder_path, ...
+               output_folder_name) ;
+end

landmark-matching/pointmatch.m

@@ -11,15 +11,21 @@ function pointmatch(central_tile_landmark_folder_path, ...
     % Front-end function to do z point-matching in the Patrick pipeline.
 
     % Deal with arguments
+    if ~exist('sample_metadata', 'var') || isempty(sample_metadata) ,
+        sample_metadata = [] ;  % only used when in debug mode
+    end
     if ~exist('manual_nominal_other_tile_ijk_offset', 'var') || isempty(manual_nominal_other_tile_ijk_offset) ,
-        manual_nominal_other_tile_ijk_offset = [] ;
+        manual_nominal_other_tile_ijk_offset = [] ;  % Means to just calculate the nominal offset
     end
     if ~exist('central_tile_ijk1', 'var') || isempty(central_tile_ijk1) ,
-        central_tile_ijk1 = [nan nan nan] ;
+        central_tile_ijk1 = [nan nan nan] ;  % only ever used for debugging, and currently not used at all
     end
     if ~exist('maximum_landmark_count', 'var') || isempty(maximum_landmark_count) ,
-        maximum_landmark_count = 1e3 ;
+        maximum_landmark_count = 1e4 ;
     end   
+    if do_run_in_debug_mode && isempty(sample_metadata) ,
+        error('sample_metadata must be nonempty in debug mode') ;
+    end
 
     % Read in stuff from input files
     central_tile_scope_struct = readScopeFile(central_tile_raw_folder_path) ;