Use memory storage only for MR data (#887)

* [ci skip] removed debugging leftovers from coil_sensitivity_maps.py

* [ci skip] covered for absent pylab in grappa_and_steepest_descent.py

* [ci skip] fixed spaces-in-path issue in MR run_all.py scripts

* [ci skip] removed MR file storage option from C++ code

* [ci skip] removed storage scheme handling from MR interfaces

* [ci skip] removed setting storage scheme from Python/MR demo scripts

* [ci skip] covered for absent pylab in PET_MCIR.py

* [ci skip] removed setting storage scheme from Python/PETMR/PET_MCIR

* [ci skip] added non-memory storage scheme warning to Gadgetron.AcquisitionData

* [ci skip] made MR acquisition data reading monitoring output more compact

* [ci skip] removed setting the storage scheme from Matlab/MR demo scripts

* [ci skip] restored erroneously removed PET storage scheme setting in PET_MCIR

* [ci skip] added non-memory storage scheme warning to +Gadgetron.AcquisitionData

* [ci skip] re-worded non-memory storage warning in Gadgetron.AcquisitionData

* [ci skip] covered for Python executables other than python.exe

* [ci skip] removed AcquisitionsVector.init()

* [ci skip] proper treatment of paths with spaces in run_all.py implemented

* [ci skip] cleaned up from commented-out lines

* [ci skip] cleaned up from commented-out lines

* [ci skip] corrected treatment of paths with spaces in MR/Gadgetron/run_all.py

* updated CHANGES.md

CHANGES.md

@@ -1,6 +1,7 @@
 # ChangeLog
 
-## vX.X.X
+## v3.0.0
+* MR acquisition data storage scheme restricted to memory only.
 * GE Signa randoms support added.
 * If the `SIRF_DATA_PATH` environment variable is set, `examples_data_path` will search for the examples data there, or in `SIRF_INSTALL_PATH/share/SIRF-<versio_major>.<version_minor>/data` directory. In MATLAB, the `example_data_path` function has the version set by CMake at install time.
 * Defines `__version__` in `sirf` python package.

examples/Matlab/MR/acquisition_data.m

@@ -28,19 +28,12 @@ function acquisition_data(engine)
 if nargin < 1
     engine = [];
 end
-% import_str = set_up_MR(engine);
-% eval(import_str)
 MR = set_up_MR(engine);
 mr_data_path = sirf.Utilities.examples_data_path('MR');
 
 % all acquisition data generated by this script will be stored in memory
 % (the input data will remain in the input file)
 AD = MR.AcquisitionData();
-scheme = AD.get_storage_scheme();
-AD.set_storage_scheme('memory');
-% does not work this way:
-% scheme = MR.AcquisitionData.get_storage_scheme();
-% MR.AcquisitionData.set_storage_scheme('memory');
 
 % read acquisitions from an HDF file
 [filename, pathname] = uigetfile('*.h5', 'Select raw data file', mr_data_path);
@@ -117,9 +110,4 @@ function acquisition_data(engine)
     'samples', 'readouts', 'coil');
 sirf.Utilities.set_window(0.1, 0.1, 0.8, 0.8)
 
-% % Reset the storage scheme to default
-% AD.set_storage_scheme('default');
-% Restore previous storage scheme
-AD.set_storage_scheme(scheme);
-
 end

examples/Matlab/MR/acquisition_model.m

@@ -29,19 +29,10 @@ function acquisition_model(engine)
 if nargin < 1
     engine = [];
 end
-% import_str = set_up_MR(engine);
-% eval(import_str)
 MR = set_up_MR(engine);
 mr_data_path = sirf.Utilities.examples_data_path('MR');
 
-% storage scheme 'file' keeps all acquisition data generated by
-% the script in scratch files deleted after the script terminates;
-% NOTE that subsequent SIRF script runs will continue to use this scheme
-% unless the acquisition data storage scheme is explicitely set to 'memory' 
-% (see using_acquisition_data.m) or Matlab is re-started
 AD = MR.AcquisitionData();
-AD.set_storage_scheme('memory');
-%AcquisitionData.set_storage_scheme('file');
 
 % acquisitions will be read from an HDF file
 [filename, pathname] = uigetfile('*.h5', 'Select raw data file', mr_data_path);
@@ -81,10 +72,6 @@ function acquisition_model(engine)
         name = char(par(p));
         fprintf('%s %d\n', name, image.info(name))
     end
-%     fprintf('flags %d\n', image.flags())
-%     fprintf('channels %d\n', image.channels())
-%     fprintf('slice %d\n', image.slice())
-%     fprintf('repetition %d\n', image.info('repetition'))
     fprintf('matrix size %dx%dx%d\n', image.matrix_size())
 end
 

examples/Python/MR/Gadgetron/run_all.py

@@ -30,6 +30,7 @@
     args = ''
     for a in range(1, narg):
         args += ' ' + sys.argv[a]
-    err = os.system(sys.executable + ' ' + i + args)
+    exe = '"' + sys.executable + '" ' + i + args
+    err = os.system(exe)
     if err:
         raise RuntimeError(i + ' failed')

examples/Python/MR/acquisition_data.py

@@ -51,10 +51,6 @@
 slcs = int(args['--slices'])
 show_plot = not args['--non-interactive']
 
-AcquisitionData.set_storage_scheme('memory')
-scheme = AcquisitionData.get_storage_scheme()
-print('storage scheme: %s' % repr(scheme))
-
 def main():
 
     # locate the input data file

examples/Python/MR/coil_sensitivity_maps.py

@@ -111,11 +111,9 @@ def main():
                   show=False)
 
     try:
-        from ismrmrdtools0 import coils
+        from ismrmrdtools import coils
     except:
         print('Inati method requires ismrmrd-python-tools')
-        import matplotlib.pyplot as plt
-        plt.show()
         return
     # calculate coil sensitivity maps using an approach suggested by 
     #   Inati SJ, Hansen MS, Kellman P.

examples/Python/MR/fully_sampled_recon.py

@@ -53,10 +53,6 @@ def main():
     # locate the input data file
     input_file = existing_filepath(data_path, data_file)
 
-    # all acquisition data generated by this script will be stored in memory
-    # (the input data will remain in the input file)
-    AcquisitionData.set_storage_scheme('memory')
-
     # MR raw data formats from different vendors can be transformed to 
     # HDF file format using siemens_to_ismrmrd, philips_to_ismrmrd or
     # bruker_to_ismrmrd on https://github.com/ismrmrd/.

examples/Python/MR/grappa_and_steepest_descent.py

@@ -132,12 +132,15 @@ def main():
                             postpone=(i < niter - 1))
 
     if niter > 1 and show_plot:
-        import pylab
-        pylab.figure()
-        pylab.plot(numpy.arange(1, niter + 1, 1), res)
-        pylab.grid()
-        pylab.title('residual norm')
-        pylab.show()
+        try:
+            import pylab
+            pylab.figure()
+            pylab.plot(numpy.arange(1, niter + 1, 1), res)
+            pylab.grid()
+            pylab.title('residual norm')
+            pylab.show()
+        except:
+            print('pylab not found')
 
     if output_file is not None:
       print('writing to %s' % output_file)

examples/Python/MR/run_all.py

@@ -30,6 +30,7 @@
     args = ''
     for a in range(1, narg):
         args += ' ' + sys.argv[a]
-    err = os.system(sys.executable + ' ' + i + args)
+    exe = '"' + sys.executable + '" ' + i + args
+    err = os.system(exe)
     if err:
         raise RuntimeError(i + ' failed')

examples/Python/PET/run_all.py

@@ -32,4 +32,7 @@
     args = ''
     for a in range(1, narg):
         args += ' ' + sys.argv[a]
-    os.system(sys.executable + ' ' + i + args)
+    exe = '"' + sys.executable + '" ' + i + args
+    err = os.system(exe)
+    if err:
+        raise RuntimeError(i + ' failed')

examples/Python/PETMR/PET_MCIR.py

@@ -74,7 +74,11 @@
 from glob import glob
 from docopt import docopt
 from sirf.Utilities import error, show_2D_array
-import pylab
+try:
+    import pylab
+    have_pylab = True
+except:
+    have_pylab = False
 import sirf.Reg as reg
 import sirf.STIR as pet
 from ccpi.optimisation.algorithms import PDHG
@@ -85,8 +89,6 @@
 from ccpi.filters import regularisers
 import numpy as np
 
-pet.AcquisitionData.set_storage_scheme('memory')
-
 __version__ = '0.1.0'
 args = docopt(__doc__, version=__version__)
 
@@ -120,7 +122,7 @@
 # Initial estimate
 initial_estimate = args['--initial']
 
-visualisations = True if args['--visualisations'] else False
+visualisations = True if args['--visualisations'] and have_pylab else False
 nifti = True if args['--nifti'] else False
 use_gpu = True if args['--gpu'] else False
 descriptive_fname = True if args['--descriptive_fname'] else False

src/Synergistic/tests/test_cSynergistic.cpp

@@ -137,7 +137,8 @@ int main(int argc, char* argv[])
             std::cout << "//                  Starting complex resampler test...\n";
             std::cout << "//------------------------------------------------------------------------ //\n";
 
-            AcquisitionsFile raw_mr(raw_mr_filename);
+			AcquisitionsVector raw_mr;
+			raw_mr.read(raw_mr_filename);
 
             std::vector<gadgetron::shared_ptr<Gadget> > gadgets;
             ADD_GADGET(gadgets, NoiseAdjustGadget);

src/xGadgetron/cGadgetron/cgadgetron.cpp

@@ -421,28 +421,6 @@ cGT_AcquisitionModelBackward(void* ptr_am, const void* ptr_acqs)
 	CATCH;
 }
 
-extern "C"
-void*
-cGT_setAcquisitionDataStorageScheme(const char* scheme)
-{
-	try{
-		if (scheme[0] == 'f' || strcmp(scheme, "default") == 0)
-			AcquisitionsFile::set_as_template();
-		else
-			AcquisitionsVector::set_as_template();
-		return (void*)new DataHandle;
-	}
-	CATCH;
-}
-
-extern "C"
-void*
-cGT_getAcquisitionDataStorageScheme()
-{
-	return charDataHandleFromCharData
-		(MRAcquisitionData::storage_scheme().c_str());
-}
-
 extern "C"
 void*
 cGT_sortAcquisitions(void* ptr_acqs)
@@ -479,17 +457,11 @@ cGT_ISMRMRDAcquisitionsFromFile(const char* file)
 {
 	if (!file_exists(file))
 		return fileNotFound(file, __FILE__, __LINE__);
-	std::string scheme = MRAcquisitionData::storage_scheme();
 	try {
-		shared_ptr<MRAcquisitionData> 
-			acquisitions(new AcquisitionsFile(file));
-		if (scheme[0] != 'm')
-			return newObjectHandle<MRAcquisitionData>(acquisitions);
-		else {
-			shared_ptr<MRAcquisitionData>
-				acqs(acquisitions->clone());
-			return newObjectHandle<MRAcquisitionData>(acqs);
-		}
+		shared_ptr<MRAcquisitionData>
+			acquisitions(new AcquisitionsVector);
+		acquisitions->read(file);
+		return newObjectHandle<MRAcquisitionData>(acquisitions);
 	}
 	CATCH;
 }
@@ -500,7 +472,8 @@ cGT_ISMRMRDAcquisitionsFile(const char* file)
 {
 	try {
 		shared_ptr<MRAcquisitionData> 
-			acquisitions(new AcquisitionsFile(file, true));
+			acquisitions(new AcquisitionsVector);
+		acquisitions->read(file);
 		return newObjectHandle<MRAcquisitionData>(acquisitions);
 	}
 	CATCH;