Allow writing complex images and attempt at imagearray writer

+gadgetron/+external/+readers/read_image_array.m

@@ -21,7 +21,7 @@
 
 function meta = read_meta_container(socket)
     size = read(socket, 1, 'uint64');
-    meta = arrayfun(@(~) gadgetron.external.readers.read_string(socket, 'uint64'), 1:size);
+    meta = arrayfun(@(~) gadgetron.external.readers.read_string(socket, 'uint64'), 1:size,'UniformOutput',false);
 end
 
 function waveform = read_optional_waveforms(socket)

+gadgetron/+external/+writers/encode_acquisition_headers.m

@@ -1,57 +1,48 @@
 function bytes = encode_acquisition_headers(headers)
 
     nheaders = numel(headers.version);
-
     bytes = zeros(340, nheaders, 'int8');
 
-    function bytes = byte_view(array)
-        bytes = typecast(reshape(array, 1, nheaders, []), 'int8');
+    function bytes = byte_view(array, width)
+        bytes = reshape( ...
+            typecast(squeeze(reshape(array, 1, [])), 'int8'), ...
+            width, [] ...
+            );
     end
 
-    bytes(  1:  2, :) = byte_view(headers.version);
-end
-
-
-
-function headers = decode_acquisition_headers(bytes, dims)
-    % Convert from a byte array to a ISMRMRD AcquisitionHeaders
-    % This conforms to the memory layout of the C-struct
-
-    bytes = reshape(bytes, 340, []);
-    N = size(bytes, 2);            
-    dims = num2cell(dims);
-
-    headers.version =                  reshape(typecast(reshape(bytes(  1:   2, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % First unsigned int indicates the version %
-    headers.flags =                    reshape(typecast(reshape(bytes(  3:  10, :), 1, 8 *      N), 'uint64'), dims{:},  1);  % bit field with flags %
-    headers.measurement_uid =          reshape(typecast(reshape(bytes(  11: 14, :), 1, 4 *      N), 'uint32'), dims{:},  1);  % Unique ID for the measurement %
-    headers.scan_counter =             reshape(typecast(reshape(bytes(  15: 18, :), 1, 4 *      N), 'uint32'), dims{:},  1);  % Current acquisition number in the measurement %
-    headers.acquisition_time_stamp =   reshape(typecast(reshape(bytes(  19: 22, :), 1, 4 *      N), 'uint32'), dims{:},  1);  % Acquisition clock %
-    headers.physiology_time_stamp =    reshape(typecast(reshape(bytes(  23: 34, :), 1, 4 *  3 * N), 'uint32'), dims{:},  3);  % Physiology time stamps, e.g. ecg, breating, etc. %
-    headers.number_of_samples =        reshape(typecast(reshape(bytes(  35: 36, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % Number of samples acquired %
-    headers.available_channels =       reshape(typecast(reshape(bytes(  37: 38, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % Available coils %
-    headers.active_channels =          reshape(typecast(reshape(bytes(  39: 40, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % Active coils on current acquisiton %
-    headers.channel_mask =             reshape(typecast(reshape(bytes(  41:168, :), 1, 8 * 16 * N), 'uint64'), dims{:}, 16);  % Mask to indicate which channels are active. Support for 1024 channels %
-    headers.discard_pre =              reshape(typecast(reshape(bytes( 169:170, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % Samples to be discarded at the beginning of acquisition %
-    headers.discard_post =             reshape(typecast(reshape(bytes( 171:172, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % Samples to be discarded at the end of acquisition %
-    headers.center_sample =            reshape(typecast(reshape(bytes( 173:174, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % Sample at the center of k-space %
-    headers.encoding_space_ref =       reshape(typecast(reshape(bytes( 175:176, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % Reference to an encoding space, typically only one per acquisition %
-    headers.trajectory_dimensions =    reshape(typecast(reshape(bytes( 177:178, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % Indicates the dimensionality of the trajectory vector (0 means no trajectory) %
-    headers.sample_time_us =           reshape(typecast(reshape(bytes( 179:182, :), 1, 4 *      N), 'single'), dims{:},  1);  % Time between samples in micro seconds, sampling BW %
-    headers.position =                 reshape(typecast(reshape(bytes( 183:194, :), 1, 4 *  3 * N), 'single'), dims{:},  3);  % Three-dimensional spatial offsets from isocenter %
-    headers.read_dir =                 reshape(typecast(reshape(bytes( 195:206, :), 1, 4 *  3 * N), 'single'), dims{:},  3);  % Directional cosines of the readout/frequency encoding %
-    headers.phase_dir =                reshape(typecast(reshape(bytes( 207:218, :), 1, 4 *  3 * N), 'single'), dims{:},  3);  % Directional cosines of the phase encoding %
-    headers.slice_dir =                reshape(typecast(reshape(bytes( 219:230, :), 1, 4 *  3 * N), 'single'), dims{:},  3);  % Directional cosines of the slice %
-    headers.patient_table_position =   reshape(typecast(reshape(bytes( 231:242, :), 1, 4 *  3 * N), 'single'), dims{:},  3);  % Patient table off-center %
-    headers.kspace_encode_step_1 =     reshape(typecast(reshape(bytes( 243:244, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % phase encoding line number %
-    headers.kspace_encode_step_2 =     reshape(typecast(reshape(bytes( 245:246, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % partition encodning number %
-    headers.average =                  reshape(typecast(reshape(bytes( 247:248, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % signal average number %
-    headers.slice =                    reshape(typecast(reshape(bytes( 249:250, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % imaging slice number %
-    headers.contrast =                 reshape(typecast(reshape(bytes( 251:252, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % echo number in multi-echo %
-    headers.phase =                    reshape(typecast(reshape(bytes( 253:254, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % cardiac phase number %
-    headers.repetition =               reshape(typecast(reshape(bytes( 255:256, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % dynamic number for dynamic scanning %
-    headers.set =                      reshape(typecast(reshape(bytes( 257:258, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % flow encoding set %
-    headers.segment =                  reshape(typecast(reshape(bytes( 259:260, :), 1, 2 *      N), 'uint16'), dims{:},  1);  % segment number for segmented acquisition %
-    headers.user =                     reshape(typecast(reshape(bytes( 261:276, :), 1, 2 *  8 * N), 'uint16'), dims{:},  8);  % Free user parameters %
-    headers.user_int =                 reshape(typecast(reshape(bytes( 277:308, :), 1, 4 *  8 * N), 'int32' ), dims{:},  8);  % Free user parameters %
-    headers.user_float =               reshape(typecast(reshape(bytes( 309:340, :), 1, 4 *  8 * N), 'single'), dims{:},  8);  % Free user parameters %
+    bytes(  1:  2, :) = byte_view(headers.version,          2);
+    bytes(  3:  10, :) = byte_view(headers.flags,           8);
+    bytes( 11:  14, :) = byte_view(headers.measurement_uid, 4);
+    bytes( 15:  18, :) = byte_view(headers.scan_counter,    4);
+    bytes( 19:  22, :) = byte_view(headers.acquisition_time_stamp,    4);
+    bytes( 23:  34, :) = byte_view(headers.physiology_time_stamp(:),    4*3);
+    bytes( 35:  36, :) = byte_view(headers.number_of_samples,    2);
+    bytes( 37:  38, :) = byte_view(headers.available_channels,    2);
+    bytes( 39:  40, :) = byte_view(headers.active_channels,    2);
+    bytes( 41:  168, :) = byte_view(headers.channel_mask,    8*16);
+    bytes( 169:  170, :) = byte_view(headers.discard_pre,    2);
+    bytes( 171:  172, :) = byte_view(headers.discard_post,    2);  
+    bytes( 173:  174, :) = byte_view(headers.center_sample,    2);
+    bytes( 175:  176, :) = byte_view(headers.encoding_space_ref,    2);
+    bytes( 177:  178, :) = byte_view(headers.trajectory_dimensions,    2);
+    bytes( 179:  182, :) = byte_view(headers.sample_time_us,    4);
+    bytes( 183:  194, :) = byte_view(headers.position,    4*3);
+    bytes( 195:  206, :) = byte_view(headers.read_dir,    4*3);
+    bytes( 207:  218, :) = byte_view(headers.phase_dir,    4*3);
+    bytes( 219:  230, :) = byte_view(headers.slice_dir,    4*3);
+    bytes( 231:  242, :) = byte_view(headers.patient_table_position,    4*3);
+    bytes( 243:  244, :) = byte_view(headers.kspace_encode_step_1,    2);
+    bytes( 245:  246, :) = byte_view(headers.kspace_encode_step_2,    2);
+    bytes( 247:  248, :) = byte_view(headers.average,    2);
+    bytes( 249:  250, :) = byte_view(headers.slice,    2);
+    bytes( 251:  252, :) = byte_view(headers.contrast,    2);
+    bytes( 253:  254, :) = byte_view(headers.phase,    2);
+    bytes( 255:  256, :) = byte_view(headers.repetition,    2);
+    bytes( 257:  258, :) = byte_view(headers.set,    2);
+    bytes( 259:  260, :) = byte_view(headers.segment,    2);
+    bytes( 261:  276, :) = byte_view(headers.user,    2*8);
+    bytes( 277:  308, :) = byte_view(headers.user_int,    4*8);
+    bytes( 309:  340, :) = byte_view(headers.user_float,    4*8);
+
+    bytes = reshape(bytes, 1, []);
 end

+gadgetron/+external/+writers/write_acq_header_array.m

@@ -0,0 +1,5 @@
+function write_acq_header_array(socket, headers)
+    gadgetron.external.writers.write_vector(socket, size(headers.version));
+    write(socket, gadgetron.external.writers.encode_acquisition_headers(headers));
+end
+

+gadgetron/+external/+writers/write_image.m

@@ -44,5 +44,13 @@ function write_attribute_string(socket, attribute_string)
 end
 
 function write_data(socket, data)
-    write(socket, reshape(data, 1, []));
+    if(isreal(data))
+        output = data;
+    else
+        output = zeros([2, size(data)], 'like',data);
+        output(1, :) = real(data(:));
+        output(2, :) = imag(data(:));
+    end
+    write(socket, reshape(output, 1, []));
+%     write(socket, reshape(data, 1, []));
 end

+gadgetron/+external/Connection.m

@@ -215,7 +215,8 @@ function add_writer(self, writer)
             writers = gadgetron.lib.list( ...
                 gadgetron.external.writers.write_image, ...
                 gadgetron.external.writers.write_acquisition, ...
-                gadgetron.external.writers.write_waveform ...
+                gadgetron.external.writers.write_waveform, ...
+                gadgetron.external.writers.write_image_array ...
             );
         end