def test_load_all_indiv(self):
"""
Load a few files with different options and check they load correctly
"""
group_name = 'all_fits_rect'
for fpath in self._fits_paths:
group = msapi.LoadFITS(Filename=fpath,
LoadAsRectImg=True,
OutputWorkspace=group_name)
group_norect_name = 'all_fits_norect'
for fpath in self._fits_paths:
group_norect = msapi.LoadFITS(Filename=fpath,
LoadAsRectImg=False,
OutputWorkspace=group_norect_name)
self.assertEquals(group.size(), group_norect.size())
for idx in range(0, group.size()):
img_a = group.getItem(idx)
size_a = img_a.getNumberHistograms() * img_a.blocksize()
img_b = group_norect.getItem(idx)
size_b = img_b.getNumberHistograms() * img_b.blocksize()
self.assertEquals(size_a, size_b)
self.assertEquals(img_a.getTitle(), img_b.getTitle())
for row in [0, 100, 200, 300, 400, 511]:
self.assertEquals(
img_a.readY(row)[0],
img_b.readY(row * img_a.blocksize() + 0))
msapi.DeleteWorkspace(group_name)
msapi.DeleteWorkspace(group_norect_name)
def test_load_save_load(self):
"""
Check that nothing is lost in a Load/Save/Load cycle
"""
group_name = 'all_indiv'
for fpath in self._fits_paths:
msapi.LoadFITS(Filename=fpath, LoadAsRectImg=True, OutputWorkspace=group_name)
group = msapi.mtd[group_name]
for idx in range(0, group.size()):
# Save
img_loaded = group.getItem(idx)
save_filename = 'test.fits'
msapi.SaveFITS(Filename=save_filename, InputWorkspace=img_loaded)
# Re-load and compare
reload_name = 'indiv_fits_reloaded'
grp_reloaded = msapi.LoadFITS(Filename=save_filename, LoadAsRectImg=True, OutputWorkspace=reload_name)
self.assertEquals(1, grp_reloaded.size())
img_reloaded = grp_reloaded.getItem(0)
self.assertEquals(img_loaded.getNumberHistograms(), img_reloaded.getNumberHistograms())
self.assertEquals(img_loaded.blocksize(), img_reloaded.blocksize())
(comp_result, tbl_messages) = msapi.CompareWorkspaces(img_loaded, img_reloaded)
num_rows = tbl_messages.rowCount()
txt_messages = [tbl_messages.row(idx) for idx in range(0, num_rows)]
self.assertTrue(comp_result,
"Workspace comparison failed. Details: {0}".format(txt_messages))
msapi.DeleteWorkspace(grp_reloaded)
msapi.DeleteWorkspace(group_name)
def setUp(self):
# example files to make a stack of images
_raw_files = ['LARMOR00005328_Metals_000_SummedImg_1.fits',
'LARMOR00005329_Metals_000_SummedImg_2.fits',
'LARMOR00005330_Metals_000_SummedImg_3.fits',
'LARMOR00005331_Metals_000_SummedImg_4.fits',
'LARMOR00005332_Metals_000_SummedImg_5.fits'
]
# a name for the stack / group of workspaces
_data_wsname = 'small_img_stack'
self.__class__.test_input_dir = 'some_imaging_test_path_in'
self.__class__.test_output_dir = 'some_imaging_test_path_out'
if not self.__class__.data_wsg:
filename_string = ",".join(_raw_files)
# Load all images into a workspace group, one matrix workspace per image
self.__class__.data_wsg = sapi.LoadFITS(Filename=filename_string,
LoadAsRectImg=True,
OutputWorkspace=_data_wsname)
self.__class__.data_vol = self._ws_group_to_data_vol(self.data_wsg)
# double-check before every test that the input workspaces are available and of the
# correct types
if not self.data_wsg or not _data_wsname in mtd:
raise RuntimeError("Input workspace not available")
# this could use assertIsInstance (new in version 2.7)
self.assertTrue(isinstance(self.data_wsg, WorkspaceGroup))
img_workspaces = [ self.data_wsg.getItem(i) for i in range(0, self.data_wsg.size()) ]
for wksp in img_workspaces:
self.assertTrue(isinstance(wksp, MatrixWorkspace))
def test_run_ok(self):
if not os.path.exists(self._out_dir):
os.mkdir(self._out_dir)
num_proj, num_bands = msapi.ImggAggregateWavelengths(InputPath = self._raw_files_dir,
OutputPath = self._out_dir)
self.assertEquals(num_proj, 4)
self.assertEquals(num_bands, 6)
# (x,y) coordinates of some pixels
ref_positions = [(44, 77), (312, 265), (480, 397), (118, 109),
(0, 0), (511, 0), (0, 511), (511, 511)]
# Their expected values in every of the output images
ref_values = [[0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0],
[2, 1, 2, 3, 6, 5, 2, 3], [5, 3, 4, 7, 4, 1, 5, 5]]
for ref_val in ref_values:
self.assertEquals(len(ref_positions), len(ref_val))
for image_idx, fname in enumerate(self._expected_out_fnames):
fname = os.path.join(self._out_dir, fname)
group_name = 'loaded_fits'
group = msapi.LoadFITS(Filename=fname, LoadAsRectImg=True, OutputWorkspace=group_name)
self.assertEquals(image_idx+1, group.size())
wks = group.getItem(group.size()-1)
self.assertEquals(wks.getNumberHistograms(), 512)
self.assertEquals(wks.blocksize(), 512)
for pos_idx, pos in enumerate(ref_positions):
self.assertEquals(wks.readY(pos[1])[pos[0]], ref_values[image_idx][pos_idx])
msapi.DeleteWorkspace(group_name)
self._cleanup_dirs_files()
def test_load_all_at_once(self):
"""
A batch load, as when stacks are loaded at once
"""
all_filepaths = ','.join(self._fits_paths)
group = msapi.LoadFITS(Filename=all_filepaths, LoadAsRectImg=True)
self.assertEquals(group.size(), len(self._fits_paths))
msapi.DeleteWorkspace(group)