attended to the reviewer comments and suggestions

examples/Python/MR/noncartesian_cg_sense.py

@@ -137,7 +137,7 @@ def main():
 
     # acquisition data will be read from an HDF file input_file
     # AcquisitionData.set_storage_scheme('memory')
-    acq_data = mr.AcquisitionData(input_file, False)
+    acq_data = mr.AcquisitionData(input_file)
 
     print('---\n acquisition data norm: %e' % acq_data.norm())
 

examples/Python/MR/noncartesian_recon.py

@@ -71,7 +71,7 @@ def main():
 
     # locate the k-space raw data file adn read
     input_file = existing_filepath(data_path, data_file)
-    acq_data = mr.AcquisitionData(input_file, False)
+    acq_data = mr.AcquisitionData(input_file)
 
     # pre-process acquisition data
     if trajtype != 'radial' and trajtype != 'goldenangle':

src/xGadgetron/cGadgetron/cgadgetron.cpp

@@ -574,7 +574,7 @@ cGT_ISMRMRDAcquisitionsFromFile(const char* file, int all, size_t ptr)
 			mask.set(0);
 		else
 			mask.set(ignored);
-		mask.show_bits();
+		std::cout << mask.bits_string() << '\n';
 		shared_ptr<MRAcquisitionData>
 			acquisitions(new AcquisitionsVector);
 		IgnoreMask copy = acquisitions->ignore_mask();

src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_data_containers.h

@@ -117,7 +117,17 @@ namespace sirf {
 
 	/*!
 	\ingroup Gadgetron Data Containers
-	\brief Class enabling ignoring certain 'irregular' acquisitions.
+	\brief Class enabling ignoring acquisitions with certain ISMRMRD acquisition flags.
+
+	Most of the acquisitiondata can be represented by a multidimensional array.
+	However, the input raw data may also contain acquisitions serving some special
+	purposes different from the rest, e.g. acquisitions with noise calibration data
+	(ISMRMRD flag 19). These may have incompatible shape, and must be ignored e.g.
+	when calculating multidimensional data dimensions or performing algebraic operations
+	on acquisition data by some reconstruction algorithms. Class IgnoreMask encapsulates
+	a 64-bit integer with non-zero bits representing 'forbidden' ISMRMRD flags, i.e. any
+	acquisition acq that has at least one of these flags in its bit field returned by
+	its acq.flags() method will be ignored.
 	*/
 	class IgnoreMask {
 	public:
@@ -156,20 +166,22 @@ namespace sirf {
 		{
 			return bits & ignore_;
 		}
-		void show_bits() const
+		std::string bits_string() const
 		{
 			unsigned int size = max_;
 			unsigned long int one = 1;
 			unsigned long int bitmask = (one << (size - 1));
+			std::stringstream str;
 			for (unsigned int i = 0; i < size; i++) {
 				if (ignore_ & (bitmask >> i))
-					std::cout << '1';
+					str << '1';
 				else
-					std::cout << '0';
+					str << '0';
 				if ((i + 1) % 4 == 0)
-					std::cout << ' ';
+					str << ' ';
 			}
-			std::cout << '\n';
+			str << '\n';
+			return str.str();
 		}
 	private:
 		unsigned long int ignore_;
@@ -722,11 +734,13 @@ namespace sirf {
 
 		/*!
 		\brief Reader for ISMRMRD::Acquisition from ISMRMRD file.
-		* filename_ismrmrd_with_ext: filename of ISMRMRD rawdata file with .h5 extension.
 		* In case the ISMRMRD::Dataset constructor throws an std::runtime_error the reader catches it,
 		* displays the message and throws it again.
-		* To avoid reading noise samples and other calibration data, IgnoreMask may be employed
-		* to exclude potentially incompatible input.
+		* To avoid reading noise samples and other calibration data, IgnoreMask may be set
+		* (see method set_ignore_mask) to exclude potentially incompatible input.
+
+		* filename_ismrmrd_with_ext: filename of ISMRMRD rawdata file with .h5 extension.
+		* all: overrider of the ignore mask - non-zero value forces reading all acquisitions.
 		*/
 		void read(const std::string& filename_ismrmrd_with_ext, int all = 0);