Zarr support

VERSION

@@ -1 +1 @@
-1.0.4
+1.0.6

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["scikit-build", "cmake", "ninja"]
+build-backend = "setuptools.build_meta"

recipe/meta.yaml

@@ -41,7 +41,8 @@ requirements:
     - opencv
     - opencv-contrib-python
     - pywavelets
-    - tifffile    
+    - tifffile
+    - zarr    
 
 about:
     home: https://github.com/tomography/tomocupy

setup.py

@@ -10,13 +10,14 @@
     packages=find_packages('src'),
     zip_safe=False,
     install_requires=[
-        'cupy',
+    	'cupy',
         'opencv-python',
         'h5py',
         'numexpr',
         'numpy',
         'pywavelets',
         'setuptools',  # for pkg_resources at runtime
         'tifffile',
+        'zarr',
     ]
 )

src/cuda/CMakeLists.txt

@@ -19,59 +19,59 @@ include_directories(${PYTHON_INCLUDE_PATH})
 set_source_files_properties(cfunc_fourierrec.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_fourierrec LANGUAGE python SOURCES cfunc_fourierrec.i cfunc_fourierrec.cu)
 swig_link_libraries(cfunc_fourierrec cudart cufft Python::Module)
-set_target_properties(cfunc_fourierrec PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_fourierrec PROPERTIES CUDA_ARCHITECTURES "75;80")
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_fourierrec.py" DESTINATION tomocupy)
 install(TARGETS cfunc_fourierrec LIBRARY DESTINATION tomocupy)
 
 set_source_files_properties(cfunc_lprec.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_lprec LANGUAGE python SOURCES cfunc_lprec.i cfunc_lprec.cu)
 swig_link_libraries(cfunc_lprec cudart cufft Python::Module)
-set_target_properties(cfunc_lprec PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_lprec PROPERTIES CUDA_ARCHITECTURES "75;80")
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_lprec.py" DESTINATION tomocupy)
 install(TARGETS cfunc_lprec LIBRARY DESTINATION tomocupy)
 
 set_source_files_properties(cfunc_linerec.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_linerec LANGUAGE python SOURCES cfunc_linerec.i cfunc_linerec.cu)
 swig_link_libraries(cfunc_linerec cudart Python::Module)
-set_target_properties(cfunc_linerec PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_linerec PROPERTIES CUDA_ARCHITECTURES "75;80")
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_linerec.py" DESTINATION tomocupy)
 install(TARGETS cfunc_linerec LIBRARY DESTINATION tomocupy)
 
 set_source_files_properties(cfunc_filter.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_filter LANGUAGE python SOURCES cfunc_filter.i cfunc_filter.cu)
 swig_link_libraries(cfunc_filter cudart cufft Python::Module)
-set_target_properties(cfunc_filter PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_filter PROPERTIES CUDA_ARCHITECTURES "75;80")
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_filter.py" DESTINATION tomocupy)
 install(TARGETS cfunc_filter LIBRARY DESTINATION tomocupy)
 
 set_source_files_properties(cfunc_fourierrecfp16.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_fourierrecfp16 LANGUAGE python SOURCES cfunc_fourierrecfp16.i cfunc_fourierrec.cu)
 swig_link_libraries(cfunc_fourierrecfp16 cudart cufft Python::Module)
-set_target_properties(cfunc_fourierrecfp16 PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_fourierrecfp16 PROPERTIES CUDA_ARCHITECTURES "75;80")
 target_compile_definitions(cfunc_fourierrecfp16 PRIVATE HALF)
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_fourierrecfp16.py" DESTINATION tomocupy)
 install(TARGETS cfunc_fourierrecfp16 LIBRARY DESTINATION tomocupy)
 
 set_source_files_properties(cfunc_lprecfp16.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_lprecfp16 LANGUAGE python SOURCES cfunc_lprecfp16.i cfunc_lprec.cu)
 swig_link_libraries(cfunc_lprecfp16 cudart cufft Python::Module)
-set_target_properties(cfunc_lprecfp16 PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_lprecfp16 PROPERTIES CUDA_ARCHITECTURES "75;80")
 target_compile_definitions(cfunc_lprecfp16 PRIVATE HALF)
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_lprecfp16.py" DESTINATION tomocupy)
 install(TARGETS cfunc_lprecfp16 LIBRARY DESTINATION tomocupy)
 
 set_source_files_properties(cfunc_linerecfp16.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_linerecfp16 LANGUAGE python SOURCES cfunc_linerecfp16.i cfunc_linerec.cu)
 swig_link_libraries(cfunc_linerecfp16 cudart Python::Module)
-set_target_properties(cfunc_linerecfp16 PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_linerecfp16 PROPERTIES CUDA_ARCHITECTURES "75;80")
 target_compile_definitions(cfunc_linerecfp16 PRIVATE HALF)
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_linerecfp16.py" DESTINATION tomocupy)
 install(TARGETS cfunc_linerecfp16 LIBRARY DESTINATION tomocupy)
 
 set_source_files_properties(cfunc_filterfp16.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_filterfp16 LANGUAGE python SOURCES cfunc_filterfp16.i cfunc_filter.cu)
 swig_link_libraries(cfunc_filterfp16 cudart cufft Python::Module)
-set_target_properties(cfunc_filterfp16 PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_filterfp16 PROPERTIES CUDA_ARCHITECTURES "75;80")
 target_compile_definitions(cfunc_filterfp16 PRIVATE HALF)
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_filterfp16.py" DESTINATION tomocupy)
 install(TARGETS cfunc_filterfp16 LIBRARY DESTINATION tomocupy)
@@ -81,22 +81,22 @@ install(TARGETS cfunc_filterfp16 LIBRARY DESTINATION tomocupy)
 set_source_files_properties(cfunc_usfft1d.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_usfft1d LANGUAGE python SOURCES cfunc_usfft1d.i cfunc_usfft1d.cu)
 swig_link_libraries(cfunc_usfft1d cudart cufft Python::Module)
-set_target_properties(cfunc_usfft1d PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_usfft1d PROPERTIES CUDA_ARCHITECTURES "75;80")
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_usfft1d.py" DESTINATION tomocupy)
 install(TARGETS cfunc_usfft1d LIBRARY DESTINATION tomocupy)
 
 # Must tell CMake that SWIG interface files are CXX files
 set_source_files_properties(cfunc_usfft2d.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_usfft2d LANGUAGE python SOURCES cfunc_usfft2d.i cfunc_usfft2d.cu)
 swig_link_libraries(cfunc_usfft2d cudart cufft Python::Module)
-set_target_properties(cfunc_usfft2d PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_usfft2d PROPERTIES CUDA_ARCHITECTURES "75;80")
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_usfft2d.py" DESTINATION tomocupy)
 install(TARGETS cfunc_usfft2d LIBRARY DESTINATION tomocupy)
 
 # Must tell CMake that SWIG interface files are CXX files
 set_source_files_properties(cfunc_fft2d.i PROPERTIES CPLUSPLUS ON)
 swig_add_library(cfunc_fft2d LANGUAGE python SOURCES cfunc_fft2d.i cfunc_fft2d.cu)
 swig_link_libraries(cfunc_fft2d cudart cufft Python::Module)
-set_target_properties(cfunc_fft2d PROPERTIES CUDA_ARCHITECTURES "60;72;75;80")
+set_target_properties(cfunc_fft2d PROPERTIES CUDA_ARCHITECTURES "75;80")
 install(FILES "${CMAKE_CURRENT_BINARY_DIR}/cfunc_fft2d.py" DESTINATION tomocupy)
 install(TARGETS cfunc_fft2d LIBRARY DESTINATION tomocupy)

src/tomocupy/config.py

@@ -224,7 +224,7 @@ def default_parameter(func, param):
         'default': 'none',
         'type': str,
         'help': "Phase retrieval correction method",
-        'choices': ['none', 'paganin', 'Gpaganin']},
+        'choices': ['none', 'paganin', 'Gpaganin', 'FourierFilter', 'farago']},
     'energy': {
         'default': 0,
         'type': float,
@@ -240,7 +240,7 @@ def default_parameter(func, param):
     'retrieve-phase-delta-beta': {
         'default': 1500.0,
         'type': float,
-        'help': "delta/beta material for Generalized Paganin"},
+        'help': "delta/beta material for Generalized Paganin & Farago"},
     'retrieve-phase-W': {
         'default': 2e-4,
         'type': float,
@@ -249,6 +249,22 @@ def default_parameter(func, param):
         'type': utils.positive_int,
         'default': 1,
         'help': "Padding with extra slices in z for phase-retrieval filtering"},
+    'FFratio': {
+        'default': 100,
+        'type': float,
+        'help': "Shape of the Fourier Filter window"},  
+    'FFdim': {
+        'default': 2,
+        'type': float,
+        'help': "1 for sinograms, 2 for projections"},  
+    'FFlog': {
+        'default': 0,
+        'type': int,
+        'help': "0/1"},
+    'FFpad': {
+        'default': 150,
+        'type': float,
+        'help': "Padding size for the Fourier Filter"},              
 }
 
 SECTIONS['rotate-proj'] = {
@@ -395,21 +411,6 @@ def default_parameter(func, param):
         'type': int,
         'default': -1,
         'help': "End row to find the rotation center"},
-    'dtype': {
-        'default': 'float32',
-        'type': str,
-        'choices': ['float32', 'float16'],
-        'help': "Data type used for reconstruction. Note float16 works with power of 2 sizes.", },
-    'save-format': {
-        'default': 'tiff',
-        'type': str,
-        'help': "Output format",
-        'choices': ['tiff', 'h5', 'h5sino', 'h5nolinks']},
-    'clear-folder': {
-        'default': 'False',
-        'type': str,
-        'help': "Clear output folder before reconstruction",
-        'choices': ['True', 'False']},
     'fbp-filter': {
         'default': 'parzen',
         'type': str,
@@ -446,6 +447,41 @@ def default_parameter(func, param):
         'type': float,
         'help': "Pixel size [microns]"},
 }
+SECTIONS['output'] ={
+    'dtype': {
+        'default': 'float32',
+        'type': str,
+        'choices': ['float32', 'float16'],
+        'help': "Data type used for reconstruction. Note float16 works with power of 2 sizes.", },
+    'save-format': {
+        'default': 'tiff',
+        'type': str,
+        'help': "Output format",
+        'choices': ['tiff', 'h5', 'h5sino', 'h5nolinks', 'zarr']},
+    'zarr-compression': {
+        'default': 'blosclz',
+        'type': str,
+        'help': "ZARR compression format",
+        'choices': ['blosclz', 'lz4', 'zstd']},    
+    'zarr-chunk': {
+        'default': '8,64,64',
+        'type': str,
+        'help': "ZARR chunk size"},
+    'large-data': {
+        'default': False,
+        'type': bool,
+        'help': "If Active it computes ldchunk chunks of angular projections"},
+    'ldchunk': {
+        'default': 10,
+        'type': int,
+        'help': "Number of angular chunks for large-data"},                  
+    'clear-folder': {
+        'default': 'False',
+        'type': str,
+        'help': "Clear output folder before reconstruction",
+        'choices': ['True', 'False']}
+}
+
 
 SECTIONS['beam-hardening'] = {
     'beam-hardening-method': {
@@ -564,9 +600,9 @@ def default_parameter(func, param):
 
 
 RECON_PARAMS = ('file-reading', 'remove-stripe',
-                'reconstruction', 'fw', 'ti', 'vo-all', 'lamino', 'reconstruction-types', 'beam-hardening')
+                'reconstruction', 'fw', 'ti', 'vo-all', 'lamino', 'reconstruction-types', 'beam-hardening', 'output')
 RECON_STEPS_PARAMS = ('file-reading', 'remove-stripe', 'reconstruction',
-                      'retrieve-phase', 'fw', 'ti', 'vo-all', 'lamino', 'reconstruction-steps-types', 'rotate-proj', 'beam-hardening')
+                      'retrieve-phase', 'fw', 'ti', 'vo-all', 'lamino', 'reconstruction-steps-types', 'rotate-proj', 'beam-hardening', 'output')
 
 NICE_NAMES = ('General', 'File reading', 'Remove stripe',
               'Remove stripe FW', 'Remove stripe Titarenko', 'Remove stripe Vo' 'Retrieve phase', 'Reconstruction')
@@ -773,7 +809,7 @@ def update_hdf_process(fname, args=None, sections=None):
                         hdf_file.require_dataset(dataset, shape=(1,), dtype=dt)
                         log.info(name + ': ' + str(value))
                         try:
-                            hdf_file[dataset][0] = np.string_(str(value))
+                            hdf_file[dataset][0] = np.bytes_(str(value))
                         except TypeError:
                             log.error(
                                 "Could not convert value {}".format(value))

src/tomocupy/dataio/reader.py

@@ -84,7 +84,7 @@ def init_sizes(self):
 
         # read data sizes and projection angles with a reader
         sizes = self.read_sizes()
-        theta = self.read_theta()
+        theta = self.read_theta(sizes['nproji'])
         nproji = sizes['nproji']
         nzi = sizes['nzi']
         ni = sizes['ni']
@@ -306,12 +306,15 @@ def read_sizes(self):
 
         return sizes
 
-    def read_theta(self):
+    def read_theta(self, projections):
         """Read projection angles (in radians)"""
 
         with h5py.File(args.file_name) as file_in:
-            theta = file_in['/exchange/theta'][:].astype('float32')/180*np.pi
-
+                if '/exchange/theta' in file_in:
+                        theta = file_in['/exchange/theta'][:].astype('float32') / 180 * np.pi
+                else:
+                        # If 'theta' doesn't exist, calculate it over the range [0, proj]
+                        theta = np.linspace(0, np.pi, projections, dtype='float32')
         return theta
 
     def read_data_chunk_to_queue(self, data_queue, ids_proj, st_z, end_z, st_n, end_n, id_z, in_dtype):