Revert "Remove legacy mode from write attributes (#289)"

This reverts commit 52a2d1a.
waltsims · Feb 4, 2024 · 6659563 · 6659563
1 parent 52a2d1a
commit 6659563
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Showing 76 changed files with 638 additions and 5,573 deletions.
diff --git a/.github/codecov.yml b/.github/codecov.yml
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_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
@@ -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
@@ -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
@@ -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
@@ -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",
-            "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": {
@@ -978,6 +900,13 @@
         }
     },
     "root": {
-        "attrs": {}
+        "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'"
+        }
     }
 }