waltsims · waltsims · Feb 4, 2024 · Feb 1, 2024 · Feb 1, 2024 · Feb 1, 2024
diff --git a/.github/codecov.yml b/.github/codecov.yml
@@ -0,0 +1,5 @@
+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
@@ -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, write_matrix
+from kwave.utils.io import write_attributes_typed, 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(filepath, legacy=True)  # TODO: update to currently breaking code after references are updated
+    write_attributes_typed(filepath)
 
 
 def save_mat_file(filepath, integer_variables, float_variables):

diff --git a/kwave/utils/io.py b/kwave/utils/io.py
@@ -1,15 +1,12 @@
-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
@@ -200,37 +197,6 @@ 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.
 
@@ -242,19 +208,7 @@ def write_attributes(filename: str, file_description: Optional[str] = None, lega
         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()
 
@@ -277,18 +231,12 @@ def write_attributes(filename: str, file_description: Optional[str] = None, lega
 
     # set additional file attributes
     with h5py.File(filename, "a") as f:
-        # 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)
+        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_flags(filename):

diff --git a/tests/h5_summary.py b/tests/h5_summary.py
@@ -19,18 +19,30 @@ def from_h5(h5_path):
         data = {}
 
         def extract_summary(name, obj):
-            np_obj = np.array(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
+
             data[name] = {
                 'dtype': str(obj.dtype),
                 'attrs': H5Summary._convert_attrs(obj.attrs),
                 'shape': list(obj.shape),
-                '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)
-                }
+                'checksums': hashes
             }
 
         with h5py.File(h5_path, 'r') as hf:
@@ -68,9 +80,9 @@ def _convert_attrs(attrs):
     def get_diff(self, other, eps=1e-8, precision=8):
         assert isinstance(other, H5Summary)
         excluded = [
-            "root['root']['attrs']['created_by']",
-            "root['root']['attrs']['creation_date']",
-            "root['root']['attrs']['file_description']",
+            "root['created_by']",
+            "root['creation_date']",
+            "root['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
@@ -4,7 +4,7 @@
 import h5py
 import numpy as np
 
-from kwave.utils.io import write_matrix, write_attributes, write_grid, write_flags
+from kwave.utils.io import write_matrix, write_attributes_typed, 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(tmp_path)
+    write_attributes_typed(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
@@ -199,6 +199,32 @@
             "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": {
@@ -299,6 +325,58 @@
             "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",
+            "10": "6b86b273ff34fce19d6b804eff5a3f5747ada4eaa22f1d49c01e52ddb7875b4b",
+            "12": "6b86b273ff34fce19d6b804eff5a3f5747ada4eaa22f1d49c01e52ddb7875b4b",
+            "14": "6b86b273ff34fce19d6b804eff5a3f5747ada4eaa22f1d49c01e52ddb7875b4b",
+            "16": "6b86b273ff34fce19d6b804eff5a3f5747ada4eaa22f1d49c01e52ddb7875b4b"
+        }
+    },
+    "minor_version": {
+        "dtype": "object",
+        "attrs": {},
+        "shape": [],
+        "checksums": {
+            "6": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35",
+            "8": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35",
+            "10": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35",
+            "12": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35",
+            "14": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35",
+            "16": "d4735e3a265e16eee03f59718b9b5d03019c07d8b6c51f90da3a666eec13ab35"
+        }
+    },
     "nonlinear_flag": {
         "dtype": "uint64",
         "attrs": {
@@ -900,13 +978,6 @@
         }
     },
     "root": {
-        "attrs": {
-            "created_by": "b'k-Wave 1.3'",
-            "creation_date": "b'16-Apr-2021-00-02-50'",
-            "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'"
-        }
+        "attrs": {}
     }
 }