atlab · cathryn1 · May 16, 2016 · May 19, 2016 · May 23, 2016 · May 24, 2016
diff --git a/.gitignore b/.gitignore
@@ -2,4 +2,5 @@
 .DS_Store
 .idea
 *__pycache__*
-*.edd-info*
+*.egg-info*
+*.asv
diff --git a/RFMapRaw_Keys.mat b/RFMapRaw_Keys.mat
diff --git a/lib/+ne7/+ip/correctRaster.m b/lib/+ne7/+ip/correctRaster.m
@@ -1,22 +1,23 @@
 function img = correctRaster(img, rasterPhase, fillFraction)
-% raster correction for resonant scanners.  
+% raster correction for resonant scanners.
 % rasterPhase is the phase different between left-right and right-left scan
-% lines. 
+% lines.
 %
-% img size [x y nSlices nFrames].   2D, 3D, 4D images also work
+% img size [x y nChannel nSlices nFrames].   2D, 3D, 4D, 5D images also work
 
-
-sz = [size(img,1) size(img,2) size(img,3) size(img,4)];
-ix = (-sz(2)/2+0.5:sz(2)/2-0.5)/(sz(2)/2);
+assert(ndims(img)<=5)
+ix = (-size(img, 2)/2+0.5:size(img, 2)/2-0.5)/(size(img, 2)/2);
 tx = asin(ix*fillFraction);  % convert index to time
-for iSlice = 1:size(img,3)
-    for iFrame = 1:size(img, 4)
-        im = img(:,:,iSlice,iFrame);
-        extrapVal = mean(im(:));
-        img(1:2:end,:,iSlice,iFrame) = interp1(ix, im(1:2:end,:)', ...
-            sin(tx'+rasterPhase)/fillFraction,'linear',extrapVal)';
-        img(2:2:end,:,iSlice,iFrame) = interp1(ix, im(2:2:end,:)', ...
-            sin(tx'-rasterPhase)/fillFraction,'linear',extrapVal)';
+for iChannel = 1:size(img, 3)
+    for iSlice = 1:size(img, 4)
+        for iFrame = 1:size(img, 5)
+            im = img(:,:, iChannel, iSlice, iFrame);
+            extrapVal = mean(im(:));
+            img(1:2:end, :, iChannel, iSlice, iFrame) = interp1(ix, im(1:2:end,:)', ...
+                sin(tx'+rasterPhase)/fillFraction,'linear',extrapVal)';
+            img(2:2:end, :, iChannel, iSlice, iFrame) = interp1(ix, im(2:2:end,:)', ...
+                sin(tx'-rasterPhase)/fillFraction,'linear',extrapVal)';
+        end
     end
 end
 end
diff --git a/lib/+ne7/+scanimage/Reader5.m b/lib/+ne7/+scanimage/Reader5.m
@@ -3,7 +3,7 @@
     %  indexed as reader(col, row, frame, slice, channel).
     %  It works with scanimage 4 and scanimage 5.
     %
-    %  The reader can then be addressed with subscripts 
+    %  The reader can then be addressed with subscripts
     %         reader(y, x, channel, slice, frame)
     %
     %  Example:
@@ -20,7 +20,7 @@
         nframes
         frames_per_file
     end
-        
+
     properties(Dependent)
         nslices
         channels
@@ -32,7 +32,7 @@
         dwell_time
         bidirectional
         fill_fraction
-        is_functional
+        fastz
     end
 
     methods
@@ -62,7 +62,7 @@
             end
         end
 
-        function f = get.is_functional(self)
+        function f = get.fastz(self)
             if self.scanimage_version == 4
                 f = 1;
                 %f = self.header.fastZEnable;
@@ -75,6 +75,8 @@
         function n = get.nslices(self)
             if self.scanimage_version == 4
                 n = self.header.stackNumSlices;
+            elseif self.header.hFastZ_enable
+                n = self.header.hFastZ_numFramesPerVolume;
             else
                 n = self.header.hStackManager_numSlices;
                 %assert(n == self.header.hFastZ_numFramesPerVolume)
@@ -138,7 +140,7 @@
                 if self.header.hFastZ_enable
                     n = self.header.hFastZ_numVolumes;
                 else
-                    n = hStackManager_framesPerSlice;
+                    n = self.header.hStackManager_framesPerSlice;
                 end
             end
 
@@ -173,23 +175,17 @@
         end
 
         function sz = size(self)
-            if self.is_functional
-                sz(1) = self.header.hRoiManager_linesPerFrame; % not sure this is lines or pixels (JR)
-                sz(2) = self.header.hRoiManager_pixelsPerLine; % not sure this is lines or pixels (JR)
-                sz(3) = self.nchannels;
-                sz(4) = self.nslices;
-                sz(5) = self.nframes;
-            else
-                sz = size(self.data);
-            end
+            sz(1) = self.header.hRoiManager_linesPerFrame; % not sure this is lines or pixels (JR)
+            sz(2) = self.header.hRoiManager_pixelsPerLine; % not sure this is lines or pixels (JR)
+            sz(3) = self.nchannels;
+            sz(4) = self.nslices;
+            sz(5) = self.nframes;
         end
 
 
         function data = subsref(self, S)
             if ~strcmp(S(1).type, '()')
                 data = builtin('subsref', self, S);
-            elseif ~self.is_functional
-                data = builtin('subsref', self.data, S);
             else
                 assert(length(S.subs)==5, 'subscript error')
                 sz = size(self);
@@ -236,7 +232,7 @@
                 k=1;
                 for i=1:length(self.stacks)
                     stackInd = find(ind(sum(self.frames_per_file(1:i-1))+1 : sum(self.frames_per_file(1:i))));
-                    for j=stackInd
+                    for j=stackInd(:)'
                         setDirectory(self.stacks{i},j);
                         f = read(self.stacks{i});
                         data(:,:,k) = f(yInd,xInd);
@@ -257,24 +253,25 @@ function compute_nframes(self)
             if self.scanimage_version == 4
                 n = self.header.acqNumFrames;
             else
-                n = (length(self.files)-1) * self.header.hScan2D_logFramesPerFile;
-
-                disp('Reading number of frames in last file...');
-                k=1; 
+                n = (length(self.files)-1) * self.header.hScan2D_logFramesPerFile * self.nchannels;
+                % Reading number of frames in last file
+                k=1;
                 while ~lastDirectory(self.stacks{end})
-                    nextDirectory(self.stacks{end}); 
-                    k=k+1; 
-                end; 
-                setDirectory(self.stacks{end},1);
-
-                n = floor((n + (k / self.nchannels)) / self.nslices);
+                    nextDirectory(self.stacks{end});
+                    k=k+1;
+                end;
+                setDirectory(self.stacks{end},1);                
+                n = n + k;
 
-%                 assert(n == round(n),'Total nframes / nslices must be an integer. Maybe scan aborted?')
             end
-            self.nframes = n;
+            self.nframes = n/self.nchannels/self.nslices;
+            if self.nframes ~= round(self.nframes)
+                warning 'Total nframes / nslices must be an integer. Maybe scan aborted?'
+                self.nframes = floor(self.nframes);
+            end
             self.frames_per_file(1:length(self.files)-1) = deal(self.header.hScan2D_logFramesPerFile * self.nchannels);
-            self.frames_per_file(length(self.files)) = n - sum(self.frames_per_file);
-
+            self.frames_per_file(length(self.files)) = self.nframes * self.nchannels * self.nslices - sum(self.frames_per_file);
+            
         end
 
         function find_files(self, path)
@@ -295,12 +292,22 @@ function load_header(self)
                 self.scanimage_version = 5;
                 temp = regexp(hdr, '^scanimage\.SI\.(?<attr>[\.\w]*)\s*=\s*(?<value>.*\S)\s*$', 'names');
             end
+            framenums = regexp(hdr, '^(?<attr>[\.frameNumbers]*)\s*=\s*(?<value>.*\S)\s*$', 'names');
+            framenums = [framenums{~cellfun(@isempty, framenums)}];
             hdr = temp;
             hdr = [hdr{~cellfun(@isempty, hdr)}];
+            if isempty(hdr) % in case we have used scanimage 5.2 
+                hdr = textscan(tiff.getTag('Software'),'%s','Delimiter',char(10));
+                hdr = strtrim(hdr{1});
+                self.scanimage_version = 5.2;
+                temp = regexp(hdr, '^SI\.(?<attr>[\.\w]*)\s*=\s*(?<value>.*\S)\s*$', 'names');
+                hdr = temp;
+                hdr = [hdr{~cellfun(@isempty, hdr)}];
+            end
+            hdr(end+1) = framenums;
             assert(~isempty(hdr), 'empty header -- possibly wrong ScanImage version.')
             self.header = cell2struct(cellfun(@(x) {evaluate(x)}, {hdr.value})', strrep({hdr.attr}, '.', '_'));
-
-
+
             function str = evaluate(str)
                 % if str is not in the form '<value>', then evaluate it.
                 if str(1)~='<' && str(end)~='>'
@@ -310,33 +317,9 @@ function load_header(self)
         end
 
         function init_stacks(self)
-            if self.is_functional
-                self.stacks = arrayfun(@(ifile) ...
-                    Tiff(self.files{ifile}), ...
-                    1:length(self.files), 'uni', false);
-
-                %self.stacks = arrayfun(@(ifile) ...
-                %    TIFFStack(self.files{ifile}, [], [self.nchannels self.nslices]), ...
-                %    1:length(self.files), 'uni', false);
-
-                %self.stacks = arrayfun(@(ifile) TIFFStack(self.files{ifile}),1:length(self.files), 'uni', false);
-            else
-                % if structural data, then load the entire stack into
-                % memory. The loaded data is initially flat and needs
-                % reshaping as well as permutation of axis as frames and
-                % slices are flipped.
-                data = [];
-                for idx = 1:length(self.files)
-                    stack = TIFFStack(self.files{idx}, [], self.nchannels);
-                    data = cat(4, data, stack(:,:,:,:));
-                end
-                sz = size(data);
-                assert(sz(4) == self.nframes * self.nslices, ...
-                    sprintf(['stack size mismatch: expected %d images but only %d '...
-                    'found -- be sure to load all files together'], self.nframes*self.nslices, sz(4)));
-                sz = [sz(1:end-1) self.nframes self.nslices];
-                self.data = permute(reshape(data, sz), [1,2,3,5,4]);
-            end
+            self.stacks = arrayfun(@(ifile) ...
+                Tiff(self.files{ifile}), ...
+                1:length(self.files), 'uni', false);
         end
 
     end

diff --git a/lib/+ne7/+ui/BW.mat b/lib/+ne7/+ui/BW.mat
diff --git a/lib/+ne7/+ui/csvlist.csv b/lib/+ne7/+ui/csvlist.csv
@@ -0,0 +1 @@
+1
diff --git a/lib/+ne7/+ui/drawCells.m b/lib/+ne7/+ui/drawCells.m
@@ -43,6 +43,12 @@ case num2cell('1':'9')
             else
                 removeOutlines
             end
+        case 91
+            h=findobj(gcf,'type','image');
+            set(h,'cdata',get(h,'cdata')*.9)
+        case 93
+            h=findobj(gcf,'type','image');
+            set(h,'cdata',get(h,'cdata')*1.1)
         case 27
             yes = questdlg('Do you wish to abort segmenting this image?','Finish segmentation', 'yes','no','no');
             if strcmpi('yes', yes)
@@ -66,6 +72,8 @@ case num2cell('1':'9')
         disp 'Shift-click to delete pixels from mask'
         disp 'Press BACKSPACE to undo'
         disp 'Press 1-9 to set brush size'
+        disp '[ to reduce brightness'
+        disp '] to increase brightness'
         disp 'Press SPACE to toggle outlines'
         disp 'Press ESC to discard all edits'
         disp 'Press ENTER to commit'

diff --git a/python/commons/bs.py b/python/commons/bs.py
@@ -2,3 +2,4 @@
 
 schema = dj.schema('dimitri_brain_state', locals())
 
+schema.spawn_missing_classes()
diff --git a/python/commons/common.py b/python/commons/common.py
@@ -3,3 +3,4 @@
 schema = dj.schema('common', locals())
 
 
+schema.spawn_missing_classes()
diff --git a/python/commons/inj.py b/python/commons/inj.py
@@ -0,0 +1,88 @@
+import datajoint as dj
+from commons import virus, mice
+
+schema = dj.schema('common_injections', locals())
+
+
+@schema
+class Site(dj.Lookup):
+    definition = """
+    # Injection target site
+
+    injection_site               : char(8) # ID
+    ---
+    """
+
+    @property
+    def contents(self):
+        yield from zip(['V1', 'dLGN', 'AL', 'LM', 'S1','S2','M1', 'PM','_Test'])
+
+
+@schema
+class AtlasStereotacticTargets(dj.Lookup):
+    definition = """
+    # Unadjusted stereotactic coordinates from the mouse brain atlas
+
+    ->Site
+    target_id                     : char(20) # ID for this set of coordinates
+    ---
+    caudal                        : double # coordinate caudal from bregma in mm
+    lateral                       : double # lateral coordinate in mm
+    ventral                       : double # coordinate ventral from cortical surface in mm
+    lambda_bregma_basedist=4.21   : double # base distance between lambda and bregma from the stereotactic atlas in mm
+    """
+    contents = [
+                ('dLGN', 'Tang2016', 2.6, 2.15, 2.7, 4.21),
+                ('dLGN', 'fabee01', 2.3, 2.25, 2.5, 4.21),  # dLGN
+                ('dLGN', 'fabee05', 2.4, 2.25, 2.6, 4.21),  # dLGN10302015
+                ('dLGN', 'fabee06', 2.5, 2.5, 2.7, 4.21),  # dLGN12032015
+                ('dLGN', 'fabee02', 2.3, 2.4, 2.7, 4.21),  # dLGNDeeper
+                ('dLGN', 'fabee03', 2.3, 2.3, 2.6, 4.21),  # dLGNmod
+                ('dLGN', 'fabee04', 2.3, 2.4, 2.6, 4.21),  # dLGNMoreVentralLateral
+                ('_Test', 'lambda', 4.21, 0, 0, 4.21),  # dLGNMoreVentralLateral
+                ('_Test', 'bregma', 0, 0, 0, 4.21),  # dLGNMoreVentralLateral
+                ]
+
+
+@schema
+class GuidanceMethod(dj.Lookup):
+    definition = """
+    # guidance method for injections
+
+    guidance                    : char(20)
+    ---
+    """
+
+    @property
+    def contents(self):
+        yield from zip(['2P','stereotactic','intrinsic','other'])
+
+@schema
+class VirusInjection(dj.Manual):
+    definition = """
+    # Virus Injection
+
+    -> mice.Mice
+    -> virus.Virus
+    -> Site
+    ---
+    -> GuidanceMethod
+    volume=null                   : double      # injection volume in nl
+    speed=null                    : double      # injection speed [nl/min]
+    toi=CURRENT_TIMESTAMP         : timestamp   # time of injection
+    """
+
+@schema
+class InjectionLocation(dj.Manual):
+    definition = """
+    # Adjusted stereotactic coordinates for injection
+
+    ->VirusInjection
+    ->AtlasStereotacticTargets
+    ---
+    lambda_bregma                 : double    # distance between lambda and bregma in mm as measured
+    caudal                        : double    # coordinate caudal from bregma in mm
+    lateral                       : double    # lateral coordinate in mm
+    ventral                       : double    # coordinate ventral from cortical surface in mm
+    adjustment                    : double    # adjustement factor to convert atlas coordinates to this injection
+    """
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,3 +2,4 @@

		schema = dj.schema('dimitri_brain_state', locals())

		schema.spawn_missing_classes()
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,3 +3,4 @@
		schema = dj.schema('common', locals())


		schema.spawn_missing_classes()