Changeset 1112 for trunk/src/phys_ima.m

Timestamp:

Jan 26, 2022, 7:37:21 PM (2 years ago)

Author:

sommeria

Message:

set_slice separated from geometrey_calib

File:

• trunk/src/phys_ima.m (modified) (4 diffs)

trunk/src/phys_ima.m

@@ -27 +27 @@
     npx=[npx siz(2)];
     npy=[npy siz(1)];
-    Calib=XmlData{icell}.GeometryCalib;
+    Calib{icell}=XmlData{icell}.GeometryCalib;
+    Slice{icell}=Calib{icell};
+    if isfield(XmlData{icell},'Slice')
+    Slice{icell}=XmlData{icell}.Slice;
+    end
     coord_x=[0.5 siz(2)-0.5];
     coord_y=[0.5 siz(1)-0.5];
@@ -34 +38 @@
     y_edge=[coord_y(1)*ones(1,npx(icell)) linspace(coord_y(1),coord_y(end),npy(icell))...
         coord_y(end)*ones(1,npx(icell)) linspace(coord_y(end),coord_y(1),npy(icell))];%y coordinates of the image edge(four sides)
-    [xcorner_new,ycorner_new]=phys_XYZ(Calib,x_edge,y_edge,ZIndex);%corresponding physical coordinates
+    [xcorner_new,ycorner_new]=phys_XYZ(Calib{icell},Slice{icell},x_edge,y_edge,ZIndex);%corresponding physical coordinates
     dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1);
     dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1);
@@ -54 +58 @@
 A_out=cell(1,numel(A));
 
-for icell=1:length(A)
-    Calib=XmlData{icell}.GeometryCalib;
+for icell=1:numel(A)
     % rescaling of the image coordinates without change of the image array
-    if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib)
+    if strcmp(Calib{icell}.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib)
         A_out{icell}=A{icell};%no transform
         Rangx=[0.5 npx-0.5];%image coordiantes of corners
         Rangy=[npy-0.5 0.5];
-        [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation
-        [~,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex);
+        [Rangx]=phys_XYZ(Calib{icell},[],Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation
+        [~,Rangy]=phys_XYZ(Calib{icell},[],[0.5 0.5],Rangy,ZIndex);
     else
         % the image needs to be interpolated to the new coordinates
         Z=0; %default
-        if isfield(Calib,'SliceCoord')&& size(Calib.SliceCoord,1)>=ZIndex %.Z= index of plane
-            SliceCoord=Calib.SliceCoord(ZIndex,:);
+        if isfield(Slice{icell},'SliceCoord')&& size(Slice{icell}.SliceCoord,1)>=ZIndex %.Z= index of plane
+            SliceCoord=Slice{icell}.SliceCoord(ZIndex,:);
             Z=SliceCoord(3);
-            if isfield(Calib, 'SliceAngle') && size(Calib.SliceAngle,1)>=ZIndex && ~isequal(Calib.SliceAngle(ZIndex,:),[0 0 0])
-                norm_plane=angle2normal(Calib.SliceAngle(ZIndex,:));
+            if isfield(Slice{icell}, 'SliceAngle') && size(Slice{icell}.SliceAngle,1)>=ZIndex && ~isequal(Slice{icell}.SliceAngle(ZIndex,:),[0 0 0])
+                norm_plane=angle2normal(Slice{icell}.SliceAngle(ZIndex,:));
                 Z=Z-(norm_plane(1)*(X-SliceCoord(1))+norm_plane(2)*(Y-SliceCoord(2)))/norm_plane(3);
             end
@@ -77 +80 @@
         yima=npy(icell)-0.5:-1:0.5;
         [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates
-        [XIMA,YIMA]=px_XYZ(XmlData{icell}.GeometryCalib,X,Y,Z);% image coordinates for each point in the real
+        [XIMA,YIMA]=px_XYZ(Calib{icell},Slice{icell},X,Y,Z);% image coordinates for each point in the real
         testuint8=isa(A{icell},'uint8');
         testuint16=isa(A{icell},'uint16');