From 40651eaf54562d0a1ccbde78d0184664281115cb Mon Sep 17 00:00:00 2001 From: allevitan Date: Mon, 14 Oct 2024 08:30:15 -0400 Subject: [PATCH] Remove the various deprication warnings related to converting h5py datasets to arrays with np.array() --- src/cdtools/tools/analysis/analysis.py | 3 +-- src/cdtools/tools/data/data.py | 23 +++++++++++---------- tests/tools/test_data.py | 28 ++++++++++++++------------ tests/tools/test_measurements.py | 2 +- 4 files changed, 29 insertions(+), 27 deletions(-) diff --git a/src/cdtools/tools/analysis/analysis.py b/src/cdtools/tools/analysis/analysis.py index d6f2f78..0fd913e 100644 --- a/src/cdtools/tools/analysis/analysis.py +++ b/src/cdtools/tools/analysis/analysis.py @@ -352,8 +352,7 @@ def synthesize_reconstructions(probes, objects, use_probe=False, obj_slice=None, else: shift = ip.find_shift(synth_obj[obj_slice],obj[obj_slice], resolution=50) - - obj = ip.sinc_subpixel_shift(obj,np.array(shift)) + obj = ip.sinc_subpixel_shift(obj, shift) if len(probe.shape) == 3: probe = t.stack([ip.sinc_subpixel_shift(p,tuple(shift)) diff --git a/src/cdtools/tools/data/data.py b/src/cdtools/tools/data/data.py index ed13542..556aa38 100644 --- a/src/cdtools/tools/data/data.py +++ b/src/cdtools/tools/data/data.py @@ -134,18 +134,18 @@ def get_sample_info(cxi_file): metadata[attr] = np.float32(s1[attr][()]) if 'unit_cell' in s1: - metadata['unit_cell'] = np.array(s1['unit_cell']).astype(np.float32) + metadata['unit_cell'] = s1['unit_cell'][()].astype(np.float32) if 'geometry_1/orientation' in s1: - orient = np.array(s1['geometry_1/orientation']).astype(np.float32) + orient = s1['geometry_1/orientation'][()].astype(np.float32) xvec = orient[:3] / np.linalg.norm(orient[:3]) yvec = orient[3:] / np.linalg.norm(orient[3:]) metadata['orientation'] = np.array([xvec,yvec, np.cross(xvec,yvec)]) if 'geometry_1/surface_normal' in s1: - snorm = np.array(s1['geometry_1/surface_normal']).astype(np.float32) + snorm = s1['geometry_1/surface_normal'][()].astype(np.float32) xvec = np.cross(np.array([0.,1.,0.]), snorm) xvec /= np.linalg.norm(xvec) yvec = np.cross(snorm, xvec) @@ -218,7 +218,7 @@ def get_detector_geometry(cxi_file): d1 = i1['detector_1'] if 'detector_1/basis_vectors' in i1: - basis_vectors = np.array(d1['basis_vectors']) + basis_vectors = d1['basis_vectors'][()] if basis_vectors.shape == (2,3): basis_vectors = basis_vectors.T else: @@ -244,11 +244,11 @@ def get_detector_geometry(cxi_file): [-x_pixel_size,0,0]]).transpose() try: - distance = np.float32(d1['distance']) + distance = np.float32(d1['distance'][()]) except: distance = None try: - corner_position = np.array(d1['corner_position']) + corner_position = d1['corner_position'][()] except: corner_position = None @@ -292,7 +292,7 @@ def get_mask(cxi_file): i1 = cxi_file['entry_1/instrument_1'] if 'detector_1/mask' in i1: - mask = np.array(i1['detector_1/mask']).astype(np.uint32) + mask = i1['detector_1/mask'][()].astype(np.uint32) mask_on = np.equal(mask,np.uint32(0)) mask_has_signal = np.equal(mask,np.uint32(0x00001000)) return np.logical_or(mask_on,mask_has_signal).astype(bool) @@ -324,7 +324,7 @@ def get_dark(cxi_file): i1 = cxi_file['entry_1/instrument_1'] if 'detector_1/data_dark' in i1: - darks = np.array(i1['detector_1/data_dark']) + darks = i1['detector_1/data_dark'][()] dims = tuple(range(len(darks.shape) - 2)) darks = np.nanmean(darks,axis=dims) else: @@ -426,7 +426,7 @@ def get_shot_to_shot_info(cxi_file, field_name): else: raise KeyError('Data is not defined within cxi file') - return np.array(cxi_file[pull_from]).astype(np.float32) + return cxi_file[pull_from][()].astype(np.float32) def get_ptycho_translations(cxi_file): @@ -851,11 +851,12 @@ def h5_to_nested_dict(h5_file): for key in h5_file.keys(): value = h5_file[key] if isinstance(value, h5py.Dataset): - arr = np.array(value) + arr = value[()] if arr.dtype == object: d[key] = arr.ravel()[0].decode('utf-8') elif arr.ndim == 0: - d[key] = arr.ravel()[0] + # TODO is this needed with arr = value[()]? + d[key] = arr.ravel()[0] else: d[key] = arr diff --git a/tests/tools/test_data.py b/tests/tools/test_data.py index 03998dd..bf048e5 100644 --- a/tests/tools/test_data.py +++ b/tests/tools/test_data.py @@ -182,11 +182,11 @@ def test_add_detector(tmp_path): # Check this directly since we want to make sure it saved # the pixel sizes d1 = f['entry_1/instrument_1/detector_1'] - read_basis = np.array(d1['basis_vectors']) - read_x_pix = np.float32(d1['x_pixel_size']) - read_y_pix = np.float32(d1['y_pixel_size']) - read_distance = np.float32(d1['distance']) - read_corner = np.array(d1['corner_position']) + read_basis = d1['basis_vectors'][()] + read_x_pix = d1['x_pixel_size'][()] + read_y_pix = d1['y_pixel_size'][()] + read_distance = d1['distance'][()] + read_corner = d1['corner_position'][()] assert np.isclose(distance, read_distance) assert np.allclose(basis, read_basis) @@ -232,8 +232,8 @@ def test_add_data(tmp_path): with h5py.File(tmp_path / 'test_add_data.cxi','r') as f: # Check this directly since we want to make sure it saved # it in all the places it should have - read_data_1 = np.array(f['entry_1/data_1/data']) - read_data_2 = np.array(f['entry_1/instrument_1/detector_1/data']) + read_data_1 = f['entry_1/data_1/data'][()] + read_data_2 = f['entry_1/instrument_1/detector_1/data'][()] read_axes = str(f['entry_1/instrument_1/detector_1/data'].attrs['axes'].decode()) assert np.allclose(fake_data, read_data_1) @@ -261,9 +261,10 @@ def test_add_shot_to_shot_info(tmp_path): with h5py.File(tmp_path / 'test_add_shot_to_shot_info.cxi') as f: # Check this directly since we want to make sure it saved # it in all the places it should have - read_analyzer_1 = np.array(f['entry_1/data_1/analyzer_angle']) - read_analyzer_2 = np.array(f['entry_1/instrument_1/detector_1/analyzer_angle']) - read_analyzer_3 = np.array(f['entry_1/sample_1/geometry_1/analyzer_angle']) + read_analyzer_1 = f['entry_1/data_1/analyzer_angle'][()] + read_analyzer_2 = \ + f['entry_1/instrument_1/detector_1/analyzer_angle'][()] + read_analyzer_3 = f['entry_1/sample_1/geometry_1/analyzer_angle'][()] assert np.allclose(analyzer, read_analyzer_1) assert np.allclose(analyzer, read_analyzer_2) @@ -280,9 +281,10 @@ def test_add_ptycho_translations(tmp_path): with h5py.File(tmp_path / 'test_add_ptycho_translations.cxi','r') as f: # Check this directly since we want to make sure it saved # it in all the places it should have - read_translations_1 = np.array(f['entry_1/data_1/translation']) - read_translations_2 = np.array(f['entry_1/instrument_1/detector_1/translation']) - read_translations_3 = np.array(f['entry_1/sample_1/geometry_1/translation']) + read_translations_1 = f['entry_1/data_1/translation'][()] + read_translations_2 = \ + f['entry_1/instrument_1/detector_1/translation'][()] + read_translations_3 = f['entry_1/sample_1/geometry_1/translation'][()] assert np.allclose(-translations, read_translations_1) assert np.allclose(-translations, read_translations_2) diff --git a/tests/tools/test_measurements.py b/tests/tools/test_measurements.py index 78eceb0..bfa06de 100644 --- a/tests/tools/test_measurements.py +++ b/tests/tools/test_measurements.py @@ -6,7 +6,7 @@ import numpy as np def test_intensity(): wavefields = t.rand((5,10,10)) + 1j * t.rand((5,10,10)) epsilon=1e-6 - np_result = np.abs(t.as_tensor(wavefields))**2 + epsilon + np_result = np.abs(wavefields.numpy())**2 + epsilon assert t.allclose(measurements.intensity(wavefields,epsilon=epsilon), t.as_tensor(np_result))