From 665956327b2b945f239b0cb81f2b4e900bd03d82 Mon Sep 17 00:00:00 2001 From: Walter Simson Date: Sun, 4 Feb 2024 09:51:59 -0800 Subject: [PATCH] Revert "Remove legacy mode from write attributes (#289)" This reverts commit 52a2d1acb701ddca8c1a3dd6c99b073b1b817d81. --- .github/codecov.yml | 5 - .../save_to_disk_func.py | 4 +- kwave/utils/io.py | 64 +++++++++++-- tests/h5_summary.py | 34 +++---- .../python_testers/h5io_test.py | 4 +- .../out_cpp_io_in_parts.json | 87 ++--------------- .../out_cpp_running_simulations.json | 87 ++--------------- .../out_ivp_3D_simulation.json | 87 ++--------------- .../out_ivp_axisymmetric_simulation.json | 87 ++--------------- .../out_ivp_binary_sensor_mask.json | 87 ++--------------- .../input_1.json | 87 ++--------------- .../input_2.json | 87 ++--------------- .../out_ivp_heterogeneous_medium.json | 87 ++--------------- .../out_ivp_homogeneous_medium.json | 87 ++--------------- .../out_ivp_loading_external_image.json | 87 ++--------------- .../out_ivp_opposing_corners_sensor_mask.json | 87 ++--------------- .../input_1.json | 87 ++--------------- .../input_2.json | 93 +++---------------- .../input_1.json | 87 ++--------------- .../input_2.json | 87 ++--------------- .../out_na_controlling_the_PML/input_1.json | 87 ++--------------- .../out_na_controlling_the_PML/input_2.json | 87 ++--------------- .../out_na_controlling_the_PML/input_3.json | 87 ++--------------- .../out_na_controlling_the_PML/input_4.json | 87 ++--------------- .../input_1.json | 87 ++--------------- .../input_2.json | 87 ++--------------- .../input_3.json | 87 ++--------------- .../out_pr_2D_FFT_line_sensor.json | 87 ++--------------- .../out_pr_2D_TR_circular_sensor.json | 87 ++--------------- .../input_1.json | 87 ++--------------- .../input_2.json | 87 ++--------------- .../out_pr_2D_TR_line_sensor.json | 87 ++--------------- .../out_pr_3D_FFT_planar_sensor.json | 87 ++--------------- .../out_sd_directional_array_elements.json | 87 ++--------------- .../input_1.json | 87 ++--------------- .../input_10.json | 87 ++--------------- .../input_11.json | 87 ++--------------- .../input_2.json | 87 ++--------------- .../input_3.json | 87 ++--------------- .../input_4.json | 87 ++--------------- .../input_5.json | 87 ++--------------- .../input_6.json | 87 ++--------------- .../input_7.json | 87 ++--------------- .../input_8.json | 87 ++--------------- .../input_9.json | 87 ++--------------- .../input_1.json | 87 ++--------------- .../input_10.json | 87 ++--------------- .../input_11.json | 87 ++--------------- .../input_2.json | 87 ++--------------- .../input_3.json | 87 ++--------------- .../input_4.json | 87 ++--------------- .../input_5.json | 87 ++--------------- .../input_6.json | 87 ++--------------- .../input_7.json | 87 ++--------------- .../input_8.json | 87 ++--------------- .../input_9.json | 87 ++--------------- .../out_sd_focussed_detector_2D.json | 87 ++--------------- .../out_sd_sensor_directivity_2D.json | 87 ++--------------- .../out_tvsp_3D_simulation.json | 87 ++--------------- .../out_tvsp_doppler_effect.json | 87 ++--------------- .../out_tvsp_homogeneous_medium_dipole.json | 87 ++--------------- .../out_tvsp_homogeneous_medium_monopole.json | 87 ++--------------- .../out_us_beam_patterns.json | 87 ++--------------- .../input_1.json | 87 ++--------------- .../input_2.json | 87 ++--------------- .../input_3.json | 87 ++--------------- .../input_4.json | 87 ++--------------- .../input_5.json | 87 ++--------------- .../input_6.json | 87 ++--------------- .../input_7.json | 87 ++--------------- .../input_8.json | 87 ++--------------- .../input_9.json | 87 ++--------------- .../out_us_bmode_phased_array/input_1.json | 87 ++--------------- .../out_us_defining_transducer.json | 87 ++--------------- .../out_us_transducer_as_sensor.json | 87 ++--------------- tests/test_cpp_io_in_parts.py | 4 +- 76 files changed, 638 insertions(+), 5573 deletions(-) delete mode 100644 .github/codecov.yml diff --git a/.github/codecov.yml b/.github/codecov.yml deleted file mode 100644 index 236a6f1d..00000000 --- a/.github/codecov.yml +++ /dev/null @@ -1,5 +0,0 @@ -coverage: - status: - project: - default: - threshold: 1% diff --git a/kwave/kWaveSimulation_helper/save_to_disk_func.py b/kwave/kWaveSimulation_helper/save_to_disk_func.py index ab38a49e..f4771034 100644 --- a/kwave/kWaveSimulation_helper/save_to_disk_func.py +++ b/kwave/kWaveSimulation_helper/save_to_disk_func.py @@ -9,7 +9,7 @@ from kwave.options.simulation_options import SimulationOptions from kwave.utils.data import scale_time from kwave.utils.dotdictionary import dotdict -from kwave.utils.io import write_attributes_typed, write_matrix +from kwave.utils.io import write_attributes, write_matrix from kwave.utils.matrix import num_dim2 from kwave.utils.tictoc import TicToc @@ -488,7 +488,7 @@ def save_h5_file(filepath, integer_variables, float_variables, hdf_compression_l del value # set additional file attributes - write_attributes_typed(filepath) + write_attributes(filepath, legacy=True) # TODO: update to currently breaking code after references are updated def save_mat_file(filepath, integer_variables, float_variables): diff --git a/kwave/utils/io.py b/kwave/utils/io.py index 1a0c06ef..da9f8237 100644 --- a/kwave/utils/io.py +++ b/kwave/utils/io.py @@ -1,12 +1,15 @@ +import logging import os import platform import socket from datetime import datetime +from typing import Optional import cv2 import h5py import numpy as np +import kwave from .conversion import cast_to_type from .data import get_date_string from .dotdictionary import dotdict @@ -197,6 +200,37 @@ def write_matrix(filename, matrix: np.ndarray, matrix_name: str, compression_lev def write_attributes_typed(filename, file_description=None): + # get literals + h5_literals = get_h5_literals() + + # get computer infor + comp_info = dotdict({ + 'date': datetime.now().strftime("%d-%b-%Y"), + 'computer_name': socket.gethostname(), + 'operating_system_type': platform.system(), + 'operating_system': platform.system() + " " + platform.release() + " " + platform.version(), + 'user_name': os.environ.get('USERNAME'), + 'matlab_version': 'N/A', + 'kwave_version': '1.3', + 'kwave_path': 'N/A', + }) + + # set file description if not provided by user + if file_description is None: + file_description = f'Input data created by {comp_info.user_name} running MATLAB ' \ + f'{comp_info.matlab_version} on {comp_info.operating_system_type}' + + # set additional file attributes + with h5py.File(filename, "a") as f: + f[h5_literals.FILE_MAJOR_VER_ATT_NAME] = h5_literals.HDF_FILE_MAJOR_VERSION + f[h5_literals.FILE_MINOR_VER_ATT_NAME] = h5_literals.HDF_FILE_MINOR_VERSION + f[h5_literals.CREATED_BY_ATT_NAME] = 'k-Wave 1.3' + f[h5_literals.FILE_DESCR_ATT_NAME] = file_description + f[h5_literals.FILE_TYPE_ATT_NAME] = h5_literals.HDF_INPUT_FILE + f[h5_literals.FILE_CREATION_DATE_ATT_NAME] = get_date_string() + + +def write_attributes(filename: str, file_description: Optional[str] = None, legacy: bool = False) -> None: """ Write attributes to a HDF5 file. @@ -208,7 +242,19 @@ def write_attributes_typed(filename, file_description=None): filename: The name of the HDF5 file. file_description: The description of the file. If not provided, a default description will be used. + legacy: If set to True, the function will use the deprecated legacy method to write attributes. + If set to False, the function will use the new typed method. Defaults to False. + + Raises: + DeprecationWarning: If legacy is set to True, a DeprecationWarning will be raised. + """ + + if not legacy: + write_attributes_typed(filename, file_description) + return + + logging.log(logging.WARN, f'{DeprecationWarning.__name__}: Attributes will soon be typed when saved and not saved ') # get literals h5_literals = get_h5_literals() @@ -231,12 +277,18 @@ def write_attributes_typed(filename, file_description=None): # set additional file attributes with h5py.File(filename, "a") as f: - f[h5_literals.FILE_MAJOR_VER_ATT_NAME] = h5_literals.HDF_FILE_MAJOR_VERSION - f[h5_literals.FILE_MINOR_VER_ATT_NAME] = h5_literals.HDF_FILE_MINOR_VERSION - f[h5_literals.CREATED_BY_ATT_NAME] = 'k-Wave 1.3' - f[h5_literals.FILE_DESCR_ATT_NAME] = file_description - f[h5_literals.FILE_TYPE_ATT_NAME] = h5_literals.HDF_INPUT_FILE - f[h5_literals.FILE_CREATION_DATE_ATT_NAME] = get_date_string() + # create a dictionary of attributes + attributes = { + h5_literals.FILE_MAJOR_VER_ATT_NAME: h5_literals.HDF_FILE_MAJOR_VERSION, + h5_literals.FILE_MINOR_VER_ATT_NAME: h5_literals.HDF_FILE_MINOR_VERSION, + h5_literals.CREATED_BY_ATT_NAME: f'k-Wave {kwave.VERSION}', + h5_literals.FILE_DESCR_ATT_NAME: file_description, + h5_literals.FILE_TYPE_ATT_NAME: h5_literals.HDF_INPUT_FILE, + h5_literals.FILE_CREATION_DATE_ATT_NAME: get_date_string(), + } + # loop through the attributes dictionary and assign each attribute to the file + for key, value in attributes.items(): + assign_str_attr(f.attrs, key, value) def write_flags(filename): diff --git a/tests/h5_summary.py b/tests/h5_summary.py index 18b7b629..a1759c6f 100644 --- a/tests/h5_summary.py +++ b/tests/h5_summary.py @@ -19,30 +19,18 @@ def from_h5(h5_path): data = {} def extract_summary(name, obj): - if obj.dtype != 'O': - py_obj = np.array(obj) - else: - # obj is a string with reference dtype ('|O') - py_obj = obj[()].decode("utf-8") - - hashes = {} - for sd in range(6, 17, 2): - # why to have " + 0" here? - # because in NumPy, there could be 0 & -0 - # while hashing we only want single type of zero - # therefore we add 0 to have only non-negative zero - if isinstance(py_obj, str): - hash = sha256(py_obj.encode()).hexdigest() - else: - hash = sha256(py_obj.round(sd) + 0).hexdigest() - - hashes[str(sd)] = hash - + np_obj = np.array(obj) data[name] = { 'dtype': str(obj.dtype), 'attrs': H5Summary._convert_attrs(obj.attrs), 'shape': list(obj.shape), - 'checksums': hashes + 'checksums': { + # why to have " + 0" here? + # because in NumPy, there could be 0 & -0 + # while hashing we only want single type of zero + # therefore we add 0 to have only non-negative zero + str(sd): sha256(np_obj.round(sd) + 0).hexdigest() for sd in range(6, 17, 2) + } } with h5py.File(h5_path, 'r') as hf: @@ -80,9 +68,9 @@ def _convert_attrs(attrs): def get_diff(self, other, eps=1e-8, precision=8): assert isinstance(other, H5Summary) excluded = [ - "root['created_by']", - "root['creation_date']", - "root['file_description']", + "root['root']['attrs']['created_by']", + "root['root']['attrs']['creation_date']", + "root['root']['attrs']['file_description']", "root['Nt']" # Skip Nt after updating kgrid logic ] own_summary = self._strip_checksums(precision) diff --git a/tests/matlab_test_data_collectors/python_testers/h5io_test.py b/tests/matlab_test_data_collectors/python_testers/h5io_test.py index d5ec15c4..a41925f8 100644 --- a/tests/matlab_test_data_collectors/python_testers/h5io_test.py +++ b/tests/matlab_test_data_collectors/python_testers/h5io_test.py @@ -4,7 +4,7 @@ import h5py import numpy as np -from kwave.utils.io import write_matrix, write_attributes_typed, write_grid, write_flags +from kwave.utils.io import write_matrix, write_attributes, write_grid, write_flags def compare_h5_attributes(local_h5_path, ref_path): @@ -62,7 +62,7 @@ def test_write_attributes(tmp_path_factory): matrix = np.single(10.0 * np.ones([1, 1])) ref_path = os.path.join(Path(__file__).parent, f"collectedValues/writeAttributes/{idx}.h5") write_matrix(tmp_path, matrix, matrix_name) - write_attributes_typed(tmp_path) + write_attributes(tmp_path) compare_h5_attributes(tmp_path, ref_path) idx = idx + 1 pass diff --git a/tests/reference_outputs/out_cpp_io_in_parts.json b/tests/reference_outputs/out_cpp_io_in_parts.json index 7ec09dde..539ee296 100644 --- a/tests/reference_outputs/out_cpp_io_in_parts.json +++ b/tests/reference_outputs/out_cpp_io_in_parts.json @@ -199,32 +199,6 @@ "16": "e4771988ad7747ce3ab562f13a2728280589e3c138f178d4bcf9c882dc7d78ad" } }, - "created_by": { - "dtype": "object", - "attrs": {}, - "shape": [], - "checksums": { - "6": "6640fe2857501271816938cd9541df3696cfa0470377c804a18d87ea1592d693", - "8": "6640fe2857501271816938cd9541df3696cfa0470377c804a18d87ea1592d693", - "10": "6640fe2857501271816938cd9541df3696cfa0470377c804a18d87ea1592d693", - "12": "6640fe2857501271816938cd9541df3696cfa0470377c804a18d87ea1592d693", - "14": "6640fe2857501271816938cd9541df3696cfa0470377c804a18d87ea1592d693", - "16": "6640fe2857501271816938cd9541df3696cfa0470377c804a18d87ea1592d693" - } - }, - "creation_date": { - "dtype": "object", - "attrs": {}, - "shape": [], - "checksums": { - "6": "ddabdc65b10c644161b859b40696f295ea200d08560165cb9df1d167536bef45", - "8": "ddabdc65b10c644161b859b40696f295ea200d08560165cb9df1d167536bef45", - "10": "ddabdc65b10c644161b859b40696f295ea200d08560165cb9df1d167536bef45", - "12": "ddabdc65b10c644161b859b40696f295ea200d08560165cb9df1d167536bef45", - "14": "ddabdc65b10c644161b859b40696f295ea200d08560165cb9df1d167536bef45", - "16": "ddabdc65b10c644161b859b40696f295ea200d08560165cb9df1d167536bef45" - } - }, "dt": { "dtype": "float32", "attrs": { @@ -325,58 +299,6 @@ "16": "af5570f5a1810b7af78caf4bc70a660f0df51e42baf91d4de5b2328de0e83dfc" } }, - "file_description": { - "dtype": "object", - "attrs": {}, - "shape": [], - "checksums": { - "6": "97273e0f179b26e2428e2d35eec3e92f1280acf86c194d9bf58d5a7d59efaea7", - "8": "97273e0f179b26e2428e2d35eec3e92f1280acf86c194d9bf58d5a7d59efaea7", - "10": "97273e0f179b26e2428e2d35eec3e92f1280acf86c194d9bf58d5a7d59efaea7", - "12": "97273e0f179b26e2428e2d35eec3e92f1280acf86c194d9bf58d5a7d59efaea7", - "14": "97273e0f179b26e2428e2d35eec3e92f1280acf86c194d9bf58d5a7d59efaea7", - "16": "97273e0f179b26e2428e2d35eec3e92f1280acf86c194d9bf58d5a7d59efaea7" - } - }, - "file_type": { - "dtype": "object", - "attrs": {}, - "shape": [], - "checksums": { - "6": "c96c6d5be8d08a12e7b5cdc1b207fa6b2430974c86803d8891675e76fd992c20", - "8": "c96c6d5be8d08a12e7b5cdc1b207fa6b2430974c86803d8891675e76fd992c20", - "10": "c96c6d5be8d08a12e7b5cdc1b207fa6b2430974c86803d8891675e76fd992c20", - "12": "c96c6d5be8d08a12e7b5cdc1b207fa6b2430974c86803d8891675e76fd992c20", - "14": "c96c6d5be8d08a12e7b5cdc1b207fa6b2430974c86803d8891675e76fd992c20", - "16": "c96c6d5be8d08a12e7b5cdc1b207fa6b2430974c86803d8891675e76fd992c20" - } - }, - "major_version": { - "dtype": "object", - "attrs": {}, - "shape": [], - "checksums": { - "6": "6b86b273ff34fce19d6b804eff5a3f5747ada4eaa22f1d49c01e52ddb7875b4b", - "8": "6b86b273ff34fce19d6b804eff5a3f5747ada4eaa22f1d49c01e52ddb7875b4b", - 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"8": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35", - "10": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35", - "12": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35", - "14": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35", - "16": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35" - } - }, "nonlinear_flag": { "dtype": "uint64", "attrs": { @@ -998,6 +920,13 @@ } }, "root": { - "attrs": {} + "attrs": { + "created_by": "b'k-Wave 1.3'", + "creation_date": "b'16-Apr-2021-00-15-38'", + "file_description": "b'Input data created by faridyagubbayli running MATLAB 9.7 (R2019b) on MACI64'", + "file_type": "b'input'", + "major_version": "b'1'", + "minor_version": "b'2'" + } } } \ No newline at end of file diff --git a/tests/test_cpp_io_in_parts.py b/tests/test_cpp_io_in_parts.py index fc7d1ddf..e3b4608f 100644 --- a/tests/test_cpp_io_in_parts.py +++ b/tests/test_cpp_io_in_parts.py @@ -16,7 +16,7 @@ from kwave.kgrid import kWaveGrid from kwave.utils.conversion import cast_to_type from kwave.utils.interp import interpolate3d -from kwave.utils.io import get_h5_literals, write_matrix, write_attributes_typed, write_flags, write_grid +from kwave.utils.io import get_h5_literals, write_matrix, write_attributes, write_flags, write_grid from kwave.utils.mapgen import make_ball from kwave.utils.matlab import matlab_find from kwave.utils.tictoc import TicToc @@ -254,7 +254,7 @@ def test_cpp_io_in_parts(): write_flags(input_file_full_path) # set additional file attributes - write_attributes_typed(input_file_full_path) + write_attributes(input_file_full_path, legacy=True) TicToc.toc()