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Merged
rhysgt merged 5 commits into from
Aug 24, 2026
Merged

feat: Add Oxford h5oina support #156

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6a5ebd1
Add Oxford h5oina support
rhysgt Aug 20, 2026
83e52d4
feat: Add Oxford h5oina support
mikesmic Aug 21, 2026
da9b2e2
feat: Support for processed dataset in h5oina
rhysgt Aug 21, 2026
e8ecfb4
fix: code typo
rhysgt Aug 21, 2026
df899d6
refactor: tidy h5 file reader
mikesmic Aug 21, 2026
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168 changes: 156 additions & 12 deletions defdap/file_readers.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -13,15 +13,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd
from abc import ABC, abstractmethod
import pathlib
import re

from typing import TextIO, Dict, List, Callable, Any, Type, Optional

import h5py
import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd

from defdap.crystal import Phase
from defdap.quat import Quat
from defdap.utils import Datastore
Expand DownExpand Up@@ -56,11 +57,14 @@ def __init__(self) -> None:
self.data_format = None

@staticmethod
def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]':
def get_loader(
data_type: str, file_name: pathlib.Path
) -> 'Type[EBSDDataLoader]':
if data_type is None:
data_type = {
'.crc': 'oxfordbinary',
'.cpr': 'oxfordbinary',
'.h5oina': 'oxfordh5',
'.ctf': 'oxfordtext',
'.ang': 'edaxang',
}.get(file_name.suffix, 'oxfordbinary')
Expand All@@ -70,6 +74,7 @@ def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]
loader = {
'oxfordbinary': OxfordBinaryLoader,
'oxfordtext': OxfordTextLoader,
'oxfordh5': Oxfordh5Loader,
'edaxang': EdaxAngLoader,
'pythondict': PythonDictLoader,
}[data_type]
Expand DownExpand Up@@ -234,6 +239,134 @@ def parse_phase() -> Phase:
self.check_data()


class Oxfordh5Loader(EBSDDataLoader):
def load(self, file_name: pathlib.Path, dataset = None) -> None:
"""Read an Oxford Instruments ``.h5oina`` orientation file.

Parameters
----------
file_name : pathlib.Path
Path to file.
dataset : str (raw or processed), optional
Dataset to load. If None, defaults to raw data.

"""
# Open data file and read in metadata
if not file_name.is_file():
raise FileNotFoundError(f"Cannot open file {file_name}")

file = h5py.File(file_name)

# This header contains all the information in the map that does not
# change with processing
raw_header = file['1']['EBSD']['Header']
shape = (int(raw_header['Y Cells'][0]), int(raw_header['X Cells'][0]))
self.loaded_metadata['shape'] = shape
self.loaded_metadata['step_size'] = float(raw_header['X Step'][0])
self.loaded_metadata['acquisition_rotation'] = Quat.from_euler_angles(
*raw_header['Specimen Orientation Euler'][0]
)

# Check if `Data Processing` dataset exists in the h5
if 'Data' in file['1']['Data Processing'] and dataset is None:
print('\n\tMultiple datasets in h5 file, defaulting to raw data.')
print(
'\tProcessed data can be accessed by passing `processed` to '
'the `dataset` argument.'
)

# Handle `raw` or `processed` selection
if dataset is None or dataset == 'raw':
root = file['1']['EBSD']
if dataset == 'processed':
if 'Data Processing' not in file['1']:
raise ValueError('No processed data in h5 file.')
if 'Data' not in file['1']['Data Processing']:
raise ValueError('No processed data in h5 file.')
root = file['1']['Data Processing']

# Phase data from relevant dataset
for phase_data in root['Header']['Phases'].values():
phase = Phase(
phase_data['Phase Name'][0].decode(),
phase_data['Laue Group'][0],
phase_data['Space Group'][0],
np.concatenate([
phase_data['Lattice Dimensions'][0],
phase_data['Lattice Angles'][0]
]))
self.loaded_metadata['phases'].append(phase)

self.check_metadata()

# Some data is only available and relevant for the raw data, for
# example band contrast
if dataset == 'raw':
raw_data = root['Data']
self.loaded_data.add(
'band_contrast',
np.array(raw_data['Band Contrast']).reshape(shape),
unit='', type='map', order=0,
plot_params={
'plot_colour_bar': True,
'cmap': 'gray',
'clabel': 'Band contrast',
}
)
self.loaded_data.add(
'band_slope',
np.array(raw_data['Band Slope']).reshape(shape),
unit='', type='map', order=0,
plot_params={
'plot_colour_bar': True,
'cmap': 'gray',
'clabel': 'Band slope',
}
)
self.loaded_data.add(
'mean_angular_deviation',
np.array(raw_data['Mean Angular Deviation']).reshape(shape),
unit='', type='map', order=0,
plot_params={
'plot_colour_bar': True,
'clabel': 'Mean angular deviation',
}
)
self.loaded_data.add(
'pattern_quality',
np.array(raw_data['Pattern Quality']).reshape(shape),
unit='', type='map', order=0,
plot_params={
'plot_colour_bar': True,
'clabel': 'Pattern quality',
}
)

# If pattern matching is performed, the cross correlation coefficient
# is useful
if dataset == 'processed' and 'Pattern Matching' in root:
pattern_data = root['Pattern Matching']['Data']
self.loaded_data.add(
'pattern_quality',
np.array(
pattern_data['Cross Correlation Coefficient']
).reshape(shape),
unit='', type='map', order=0,
plot_params={
'plot_colour_bar': True,
'clabel': 'Cross Correlation Coefficient',
}
)

# Get Euler angles from relevant dataset
self.loaded_data.phase = np.array(root['Data']['Phase']).reshape(shape)
self.loaded_data.euler_angle = (
root['Data']['Euler'][:].reshape(shape + (3,)).transpose((2, 0, 1))
)

self.check_data()


class EdaxAngLoader(EBSDDataLoader):
def load(self, file_name: pathlib.Path) -> None:
""" Read an EDAX .ang file.
Expand DownExpand Up@@ -327,7 +460,9 @@ def load(self, file_name: pathlib.Path) -> None:
)
add_phase = 1 if data['phase'].min() == 0 else 0
self.loaded_data.phase = data['phase'].reshape(shape) + add_phase
self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
self.loaded_data['phase', 'plot_params']['vmax'] = len(
self.loaded_metadata['phases']
)

# flatten the structured dtype
euler_angle = structured_to_unstructured(
Expand DownExpand Up@@ -424,8 +559,10 @@ def parse_line(line: str, group_dict: Dict) -> None:

group_name = group_pat.match(line.strip()).group(1)
group_dict = dict()
read_until_string(cpr_file, '[', comment_char=comment_char,
line_process=lambda l: parse_line(l, group_dict))
read_until_string(
cpr_file, '[', comment_char=comment_char,
line_process=lambda l: parse_line(l, group_dict)
)
metadata[group_name] = group_dict

# Create phase objects and move metadata to object metadata dict
Expand DownExpand Up@@ -549,7 +686,8 @@ def load_oxford_crc(self, file_name: pathlib.Path) -> None:
data[['ph1', 'phi', 'ph2']].reshape(shape)).transpose((2, 0, 1))

if self.loaded_metadata['edx']['Count'] > 0:
EDXFields = [key for key in data.dtype.fields.keys() if key.startswith('EDX')]
EDXFields = [key for key in data.dtype.fields.keys()
if key.startswith('EDX')]
for field in EDXFields:
self.loaded_data.add(
field,
Expand DownExpand Up@@ -590,7 +728,9 @@ def load(self, data_dict: Dict[str, Any]) -> None:
unit='', type='map', order=0
)
self.loaded_data.phase = data_dict['phase']
self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
self.loaded_data['phase', 'plot_params']['vmax'] = len(
self.loaded_metadata['phases']
)
self.loaded_data.euler_angle = data_dict['euler_angle']
self.check_data()

Expand DownExpand Up@@ -819,8 +959,12 @@ def load(self, file_name: pathlib.Path) -> None:

# if y descending, flip
if np.all(np.diff(data['y'][:,0])) > 0:
self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
self.loaded_data.coordinate = np.array(
[data['x'][::-1], data['y'][::-1]]
)
self.loaded_data.displacement = np.array(
[data['u'][::-1], data['v'][::-1]]
)
else:
self.loaded_data.coordinate = np.array([data['x'], data['y']])
self.loaded_data.displacement = np.array([data['u'], data['v']])
Expand Down
1 change: 1 addition & 0 deletions pyproject.toml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -41,6 +41,7 @@ dependencies = [
"matplotlib_scalebar",
"networkx",
"numba",
"h5py"
]

[project.urls]
Expand Down
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
feat: Add Oxford h5oina support by rhysgt · Pull Request #156 · MechMicroMan/DefDAP · GitHub
Skip to content
feat: Add Oxford h5oina support#156

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 Merged

rhysgt
merged 5 commits into

from

Aug 24, 2026
 Merged


feat: Add Oxford h5oina support
#156
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6a5ebd1

Add Oxford h5oina support


rhysgt Aug 20, 2026
83e52d4

feat: Add Oxford h5oina support


mikesmic Aug 21, 2026
da9b2e2

feat: Support for processed dataset in h5oina


rhysgt Aug 21, 2026
e8ecfb4

fix: code typo


rhysgt Aug 21, 2026
df899d6

refactor: tidy h5 file reader


mikesmic Aug 21, 2026

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168 changes: 156 additions & 12 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,15 +13,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd
from abc import ABC, abstractmethod
import pathlib
import re

from typing import TextIO, Dict, List, Callable, Any, Type, Optional

import h5py
import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd

from defdap.crystal import Phase
from defdap.quat import Quat
from defdap.utils import Datastore
Expand DownExpand Up@@ -56,11 +57,14 @@ def __init__(self) -> None:
 self.data_format = None

 @staticmethod
 def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]':
 def get_loader(
 data_type: str, file_name: pathlib.Path
 ) -> 'Type[EBSDDataLoader]':
 if data_type is None:
 data_type = {
 '.crc': 'oxfordbinary',
 '.cpr': 'oxfordbinary',
 '.h5oina': 'oxfordh5',
 '.ctf': 'oxfordtext',
 '.ang': 'edaxang',
 }.get(file_name.suffix, 'oxfordbinary')
Expand All@@ -70,6 +74,7 @@ def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]
 loader = {
 'oxfordbinary': OxfordBinaryLoader,
 'oxfordtext': OxfordTextLoader,
 'oxfordh5': Oxfordh5Loader,
 'edaxang': EdaxAngLoader,
 'pythondict': PythonDictLoader,
 }[data_type]
Expand DownExpand Up@@ -234,6 +239,134 @@ def parse_phase() -> Phase:
 self.check_data()


class Oxfordh5Loader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path, dataset = None) -> None:
 """Read an Oxford Instruments ``.h5oina`` orientation file.

 Parameters
 ----------
 file_name : pathlib.Path
 Path to file.
 dataset : str (raw or processed), optional
 Dataset to load. If None, defaults to raw data.

 """
 # Open data file and read in metadata
 if not file_name.is_file():
 raise FileNotFoundError(f"Cannot open file {file_name}")

 file = h5py.File(file_name)

 # This header contains all the information in the map that does not 
 # change with processing
 raw_header = file['1']['EBSD']['Header']
 shape = (int(raw_header['Y Cells'][0]), int(raw_header['X Cells'][0]))
 self.loaded_metadata['shape'] = shape
 self.loaded_metadata['step_size'] = float(raw_header['X Step'][0])
 self.loaded_metadata['acquisition_rotation'] = Quat.from_euler_angles(
 *raw_header['Specimen Orientation Euler'][0]
 )

 # Check if `Data Processing` dataset exists in the h5
 if 'Data' in file['1']['Data Processing'] and dataset is None:
 print('\n\tMultiple datasets in h5 file, defaulting to raw data.')
 print(
 '\tProcessed data can be accessed by passing `processed` to '
 'the `dataset` argument.'
 )

 # Handle `raw` or `processed` selection
 if dataset is None or dataset == 'raw':
 root = file['1']['EBSD']
 if dataset == 'processed':
 if 'Data Processing' not in file['1']:
 raise ValueError('No processed data in h5 file.')
 if 'Data' not in file['1']['Data Processing']:
 raise ValueError('No processed data in h5 file.')
 root = file['1']['Data Processing']

 # Phase data from relevant dataset
 for phase_data in root['Header']['Phases'].values():
 phase = Phase(
 phase_data['Phase Name'][0].decode(),
 phase_data['Laue Group'][0],
 phase_data['Space Group'][0],
 np.concatenate([
 phase_data['Lattice Dimensions'][0],
 phase_data['Lattice Angles'][0]
 ]))
 self.loaded_metadata['phases'].append(phase)

 self.check_metadata()

 # Some data is only available and relevant for the raw data, for 
 # example band contrast
 if dataset == 'raw':
 raw_data = root['Data']
 self.loaded_data.add(
 'band_contrast', 
 np.array(raw_data['Band Contrast']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }
 )
 self.loaded_data.add(
 'band_slope', 
 np.array(raw_data['Band Slope']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band slope',
 }
 )
 self.loaded_data.add(
 'mean_angular_deviation', 
 np.array(raw_data['Mean Angular Deviation']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Mean angular deviation',
 }
 )
 self.loaded_data.add(
 'pattern_quality', 
 np.array(raw_data['Pattern Quality']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Pattern quality',
 }
 )

 # If pattern matching is performed, the cross correlation coefficient 
 # is useful
 if dataset == 'processed' and 'Pattern Matching' in root:
 pattern_data = root['Pattern Matching']['Data']
 self.loaded_data.add(
 'pattern_quality', 
 np.array(
 pattern_data['Cross Correlation Coefficient']
 ).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Cross Correlation Coefficient',
 }
 )

 # Get Euler angles from relevant dataset
 self.loaded_data.phase = np.array(root['Data']['Phase']).reshape(shape)
 self.loaded_data.euler_angle = (
 root['Data']['Euler'][:].reshape(shape + (3,)).transpose((2, 0, 1))
 )

 self.check_data()


class EdaxAngLoader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path) -> None:
 """ Read an EDAX .ang file.
Expand DownExpand Up@@ -327,7 +460,9 @@ def load(self, file_name: pathlib.Path) -> None:
 )
 add_phase = 1 if data['phase'].min() == 0 else 0
 self.loaded_data.phase = data['phase'].reshape(shape) + add_phase
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )

 # flatten the structured dtype
 euler_angle = structured_to_unstructured(
Expand DownExpand Up@@ -424,8 +559,10 @@ def parse_line(line: str, group_dict: Dict) -> None:

 group_name = group_pat.match(line.strip()).group(1)
 group_dict = dict()
 read_until_string(cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict))
 read_until_string(
 cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict)
 )
 metadata[group_name] = group_dict

 # Create phase objects and move metadata to object metadata dict
Expand DownExpand Up@@ -549,7 +686,8 @@ def load_oxford_crc(self, file_name: pathlib.Path) -> None:
 data[['ph1', 'phi', 'ph2']].reshape(shape)).transpose((2, 0, 1))

 if self.loaded_metadata['edx']['Count'] > 0:
 EDXFields = [key for key in data.dtype.fields.keys() if key.startswith('EDX')]
 EDXFields = [key for key in data.dtype.fields.keys() 
 if key.startswith('EDX')]
 for field in EDXFields:
 self.loaded_data.add(
 field,
Expand DownExpand Up@@ -590,7 +728,9 @@ def load(self, data_dict: Dict[str, Any]) -> None:
 unit='', type='map', order=0
 )
 self.loaded_data.phase = data_dict['phase']
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )
 self.loaded_data.euler_angle = data_dict['euler_angle']
 self.check_data()

Expand DownExpand Up@@ -819,8 +959,12 @@ def load(self, file_name: pathlib.Path) -> None:

 # if y descending, flip
 if np.all(np.diff(data['y'][:,0])) > 0:
 self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
 self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
 self.loaded_data.coordinate = np.array(
 [data['x'][::-1], data['y'][::-1]]
 )
 self.loaded_data.displacement = np.array(
 [data['u'][::-1], data['v'][::-1]]
 )
 else:
 self.loaded_data.coordinate = np.array([data['x'], data['y']])
 self.loaded_data.displacement = np.array([data['u'], data['v']])
Expand Down

1 change: 1 addition & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -41,6 +41,7 @@ dependencies = [
 "matplotlib_scalebar",
 "networkx",
 "numba",
 "h5py"
]

[project.urls]
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
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.markdown-body blockquote { border-left-color: #8b949e; }
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document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
feat: Add Oxford h5oina support by rhysgt · Pull Request #156 · MechMicroMan/DefDAP · GitHub
Skip to content
feat: Add Oxford h5oina support#156

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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 Merged

rhysgt
merged 5 commits into

from

Aug 24, 2026
 Merged


feat: Add Oxford h5oina support
#156
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6a5ebd1

Add Oxford h5oina support


rhysgt Aug 20, 2026
83e52d4

feat: Add Oxford h5oina support


mikesmic Aug 21, 2026
da9b2e2

feat: Support for processed dataset in h5oina


rhysgt Aug 21, 2026
e8ecfb4

fix: code typo


rhysgt Aug 21, 2026
df899d6

refactor: tidy h5 file reader


mikesmic Aug 21, 2026

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168 changes: 156 additions & 12 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,15 +13,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd
from abc import ABC, abstractmethod
import pathlib
import re

from typing import TextIO, Dict, List, Callable, Any, Type, Optional

import h5py
import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd

from defdap.crystal import Phase
from defdap.quat import Quat
from defdap.utils import Datastore
Expand DownExpand Up@@ -56,11 +57,14 @@ def __init__(self) -> None:
 self.data_format = None

 @staticmethod
 def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]':
 def get_loader(
 data_type: str, file_name: pathlib.Path
 ) -> 'Type[EBSDDataLoader]':
 if data_type is None:
 data_type = {
 '.crc': 'oxfordbinary',
 '.cpr': 'oxfordbinary',
 '.h5oina': 'oxfordh5',
 '.ctf': 'oxfordtext',
 '.ang': 'edaxang',
 }.get(file_name.suffix, 'oxfordbinary')
Expand All@@ -70,6 +74,7 @@ def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]
 loader = {
 'oxfordbinary': OxfordBinaryLoader,
 'oxfordtext': OxfordTextLoader,
 'oxfordh5': Oxfordh5Loader,
 'edaxang': EdaxAngLoader,
 'pythondict': PythonDictLoader,
 }[data_type]
Expand DownExpand Up@@ -234,6 +239,134 @@ def parse_phase() -> Phase:
 self.check_data()


class Oxfordh5Loader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path, dataset = None) -> None:
 """Read an Oxford Instruments ``.h5oina`` orientation file.

 Parameters
 ----------
 file_name : pathlib.Path
 Path to file.
 dataset : str (raw or processed), optional
 Dataset to load. If None, defaults to raw data.

 """
 # Open data file and read in metadata
 if not file_name.is_file():
 raise FileNotFoundError(f"Cannot open file {file_name}")

 file = h5py.File(file_name)

 # This header contains all the information in the map that does not 
 # change with processing
 raw_header = file['1']['EBSD']['Header']
 shape = (int(raw_header['Y Cells'][0]), int(raw_header['X Cells'][0]))
 self.loaded_metadata['shape'] = shape
 self.loaded_metadata['step_size'] = float(raw_header['X Step'][0])
 self.loaded_metadata['acquisition_rotation'] = Quat.from_euler_angles(
 *raw_header['Specimen Orientation Euler'][0]
 )

 # Check if `Data Processing` dataset exists in the h5
 if 'Data' in file['1']['Data Processing'] and dataset is None:
 print('\n\tMultiple datasets in h5 file, defaulting to raw data.')
 print(
 '\tProcessed data can be accessed by passing `processed` to '
 'the `dataset` argument.'
 )

 # Handle `raw` or `processed` selection
 if dataset is None or dataset == 'raw':
 root = file['1']['EBSD']
 if dataset == 'processed':
 if 'Data Processing' not in file['1']:
 raise ValueError('No processed data in h5 file.')
 if 'Data' not in file['1']['Data Processing']:
 raise ValueError('No processed data in h5 file.')
 root = file['1']['Data Processing']

 # Phase data from relevant dataset
 for phase_data in root['Header']['Phases'].values():
 phase = Phase(
 phase_data['Phase Name'][0].decode(),
 phase_data['Laue Group'][0],
 phase_data['Space Group'][0],
 np.concatenate([
 phase_data['Lattice Dimensions'][0],
 phase_data['Lattice Angles'][0]
 ]))
 self.loaded_metadata['phases'].append(phase)

 self.check_metadata()

 # Some data is only available and relevant for the raw data, for 
 # example band contrast
 if dataset == 'raw':
 raw_data = root['Data']
 self.loaded_data.add(
 'band_contrast', 
 np.array(raw_data['Band Contrast']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }
 )
 self.loaded_data.add(
 'band_slope', 
 np.array(raw_data['Band Slope']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band slope',
 }
 )
 self.loaded_data.add(
 'mean_angular_deviation', 
 np.array(raw_data['Mean Angular Deviation']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Mean angular deviation',
 }
 )
 self.loaded_data.add(
 'pattern_quality', 
 np.array(raw_data['Pattern Quality']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Pattern quality',
 }
 )

 # If pattern matching is performed, the cross correlation coefficient 
 # is useful
 if dataset == 'processed' and 'Pattern Matching' in root:
 pattern_data = root['Pattern Matching']['Data']
 self.loaded_data.add(
 'pattern_quality', 
 np.array(
 pattern_data['Cross Correlation Coefficient']
 ).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Cross Correlation Coefficient',
 }
 )

 # Get Euler angles from relevant dataset
 self.loaded_data.phase = np.array(root['Data']['Phase']).reshape(shape)
 self.loaded_data.euler_angle = (
 root['Data']['Euler'][:].reshape(shape + (3,)).transpose((2, 0, 1))
 )

 self.check_data()


class EdaxAngLoader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path) -> None:
 """ Read an EDAX .ang file.
Expand DownExpand Up@@ -327,7 +460,9 @@ def load(self, file_name: pathlib.Path) -> None:
 )
 add_phase = 1 if data['phase'].min() == 0 else 0
 self.loaded_data.phase = data['phase'].reshape(shape) + add_phase
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )

 # flatten the structured dtype
 euler_angle = structured_to_unstructured(
Expand DownExpand Up@@ -424,8 +559,10 @@ def parse_line(line: str, group_dict: Dict) -> None:

 group_name = group_pat.match(line.strip()).group(1)
 group_dict = dict()
 read_until_string(cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict))
 read_until_string(
 cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict)
 )
 metadata[group_name] = group_dict

 # Create phase objects and move metadata to object metadata dict
Expand DownExpand Up@@ -549,7 +686,8 @@ def load_oxford_crc(self, file_name: pathlib.Path) -> None:
 data[['ph1', 'phi', 'ph2']].reshape(shape)).transpose((2, 0, 1))

 if self.loaded_metadata['edx']['Count'] > 0:
 EDXFields = [key for key in data.dtype.fields.keys() if key.startswith('EDX')]
 EDXFields = [key for key in data.dtype.fields.keys() 
 if key.startswith('EDX')]
 for field in EDXFields:
 self.loaded_data.add(
 field,
Expand DownExpand Up@@ -590,7 +728,9 @@ def load(self, data_dict: Dict[str, Any]) -> None:
 unit='', type='map', order=0
 )
 self.loaded_data.phase = data_dict['phase']
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )
 self.loaded_data.euler_angle = data_dict['euler_angle']
 self.check_data()

Expand DownExpand Up@@ -819,8 +959,12 @@ def load(self, file_name: pathlib.Path) -> None:

 # if y descending, flip
 if np.all(np.diff(data['y'][:,0])) > 0:
 self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
 self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
 self.loaded_data.coordinate = np.array(
 [data['x'][::-1], data['y'][::-1]]
 )
 self.loaded_data.displacement = np.array(
 [data['u'][::-1], data['v'][::-1]]
 )
 else:
 self.loaded_data.coordinate = np.array([data['x'], data['y']])
 self.loaded_data.displacement = np.array([data['u'], data['v']])
Expand Down

1 change: 1 addition & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -41,6 +41,7 @@ dependencies = [
 "matplotlib_scalebar",
 "networkx",
 "numba",
 "h5py"
]

[project.urls]
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
feat: Add Oxford h5oina support by rhysgt · Pull Request #156 · MechMicroMan/DefDAP · GitHub
Skip to content
feat: Add Oxford h5oina support#156

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 Merged

rhysgt
merged 5 commits into

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Aug 24, 2026
 Merged


feat: Add Oxford h5oina support
#156
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6a5ebd1

Add Oxford h5oina support


rhysgt Aug 20, 2026
83e52d4

feat: Add Oxford h5oina support


mikesmic Aug 21, 2026
da9b2e2

feat: Support for processed dataset in h5oina


rhysgt Aug 21, 2026
e8ecfb4

fix: code typo


rhysgt Aug 21, 2026
df899d6

refactor: tidy h5 file reader


mikesmic Aug 21, 2026

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168 changes: 156 additions & 12 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,15 +13,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd
from abc import ABC, abstractmethod
import pathlib
import re

from typing import TextIO, Dict, List, Callable, Any, Type, Optional

import h5py
import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd

from defdap.crystal import Phase
from defdap.quat import Quat
from defdap.utils import Datastore
Expand DownExpand Up@@ -56,11 +57,14 @@ def __init__(self) -> None:
 self.data_format = None

 @staticmethod
 def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]':
 def get_loader(
 data_type: str, file_name: pathlib.Path
 ) -> 'Type[EBSDDataLoader]':
 if data_type is None:
 data_type = {
 '.crc': 'oxfordbinary',
 '.cpr': 'oxfordbinary',
 '.h5oina': 'oxfordh5',
 '.ctf': 'oxfordtext',
 '.ang': 'edaxang',
 }.get(file_name.suffix, 'oxfordbinary')
Expand All@@ -70,6 +74,7 @@ def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]
 loader = {
 'oxfordbinary': OxfordBinaryLoader,
 'oxfordtext': OxfordTextLoader,
 'oxfordh5': Oxfordh5Loader,
 'edaxang': EdaxAngLoader,
 'pythondict': PythonDictLoader,
 }[data_type]
Expand DownExpand Up@@ -234,6 +239,134 @@ def parse_phase() -> Phase:
 self.check_data()


class Oxfordh5Loader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path, dataset = None) -> None:
 """Read an Oxford Instruments ``.h5oina`` orientation file.

 Parameters
 ----------
 file_name : pathlib.Path
 Path to file.
 dataset : str (raw or processed), optional
 Dataset to load. If None, defaults to raw data.

 """
 # Open data file and read in metadata
 if not file_name.is_file():
 raise FileNotFoundError(f"Cannot open file {file_name}")

 file = h5py.File(file_name)

 # This header contains all the information in the map that does not 
 # change with processing
 raw_header = file['1']['EBSD']['Header']
 shape = (int(raw_header['Y Cells'][0]), int(raw_header['X Cells'][0]))
 self.loaded_metadata['shape'] = shape
 self.loaded_metadata['step_size'] = float(raw_header['X Step'][0])
 self.loaded_metadata['acquisition_rotation'] = Quat.from_euler_angles(
 *raw_header['Specimen Orientation Euler'][0]
 )

 # Check if `Data Processing` dataset exists in the h5
 if 'Data' in file['1']['Data Processing'] and dataset is None:
 print('\n\tMultiple datasets in h5 file, defaulting to raw data.')
 print(
 '\tProcessed data can be accessed by passing `processed` to '
 'the `dataset` argument.'
 )

 # Handle `raw` or `processed` selection
 if dataset is None or dataset == 'raw':
 root = file['1']['EBSD']
 if dataset == 'processed':
 if 'Data Processing' not in file['1']:
 raise ValueError('No processed data in h5 file.')
 if 'Data' not in file['1']['Data Processing']:
 raise ValueError('No processed data in h5 file.')
 root = file['1']['Data Processing']

 # Phase data from relevant dataset
 for phase_data in root['Header']['Phases'].values():
 phase = Phase(
 phase_data['Phase Name'][0].decode(),
 phase_data['Laue Group'][0],
 phase_data['Space Group'][0],
 np.concatenate([
 phase_data['Lattice Dimensions'][0],
 phase_data['Lattice Angles'][0]
 ]))
 self.loaded_metadata['phases'].append(phase)

 self.check_metadata()

 # Some data is only available and relevant for the raw data, for 
 # example band contrast
 if dataset == 'raw':
 raw_data = root['Data']
 self.loaded_data.add(
 'band_contrast', 
 np.array(raw_data['Band Contrast']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }
 )
 self.loaded_data.add(
 'band_slope', 
 np.array(raw_data['Band Slope']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band slope',
 }
 )
 self.loaded_data.add(
 'mean_angular_deviation', 
 np.array(raw_data['Mean Angular Deviation']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Mean angular deviation',
 }
 )
 self.loaded_data.add(
 'pattern_quality', 
 np.array(raw_data['Pattern Quality']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Pattern quality',
 }
 )

 # If pattern matching is performed, the cross correlation coefficient 
 # is useful
 if dataset == 'processed' and 'Pattern Matching' in root:
 pattern_data = root['Pattern Matching']['Data']
 self.loaded_data.add(
 'pattern_quality', 
 np.array(
 pattern_data['Cross Correlation Coefficient']
 ).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Cross Correlation Coefficient',
 }
 )

 # Get Euler angles from relevant dataset
 self.loaded_data.phase = np.array(root['Data']['Phase']).reshape(shape)
 self.loaded_data.euler_angle = (
 root['Data']['Euler'][:].reshape(shape + (3,)).transpose((2, 0, 1))
 )

 self.check_data()


class EdaxAngLoader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path) -> None:
 """ Read an EDAX .ang file.
Expand DownExpand Up@@ -327,7 +460,9 @@ def load(self, file_name: pathlib.Path) -> None:
 )
 add_phase = 1 if data['phase'].min() == 0 else 0
 self.loaded_data.phase = data['phase'].reshape(shape) + add_phase
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )

 # flatten the structured dtype
 euler_angle = structured_to_unstructured(
Expand DownExpand Up@@ -424,8 +559,10 @@ def parse_line(line: str, group_dict: Dict) -> None:

 group_name = group_pat.match(line.strip()).group(1)
 group_dict = dict()
 read_until_string(cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict))
 read_until_string(
 cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict)
 )
 metadata[group_name] = group_dict

 # Create phase objects and move metadata to object metadata dict
Expand DownExpand Up@@ -549,7 +686,8 @@ def load_oxford_crc(self, file_name: pathlib.Path) -> None:
 data[['ph1', 'phi', 'ph2']].reshape(shape)).transpose((2, 0, 1))

 if self.loaded_metadata['edx']['Count'] > 0:
 EDXFields = [key for key in data.dtype.fields.keys() if key.startswith('EDX')]
 EDXFields = [key for key in data.dtype.fields.keys() 
 if key.startswith('EDX')]
 for field in EDXFields:
 self.loaded_data.add(
 field,
Expand DownExpand Up@@ -590,7 +728,9 @@ def load(self, data_dict: Dict[str, Any]) -> None:
 unit='', type='map', order=0
 )
 self.loaded_data.phase = data_dict['phase']
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )
 self.loaded_data.euler_angle = data_dict['euler_angle']
 self.check_data()

Expand DownExpand Up@@ -819,8 +959,12 @@ def load(self, file_name: pathlib.Path) -> None:

 # if y descending, flip
 if np.all(np.diff(data['y'][:,0])) > 0:
 self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
 self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
 self.loaded_data.coordinate = np.array(
 [data['x'][::-1], data['y'][::-1]]
 )
 self.loaded_data.displacement = np.array(
 [data['u'][::-1], data['v'][::-1]]
 )
 else:
 self.loaded_data.coordinate = np.array([data['x'], data['y']])
 self.loaded_data.displacement = np.array([data['u'], data['v']])
Expand Down

1 change: 1 addition & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -41,6 +41,7 @@ dependencies = [
 "matplotlib_scalebar",
 "networkx",
 "numba",
 "h5py"
]

[project.urls]
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
feat: Add Oxford h5oina support by rhysgt · Pull Request #156 · MechMicroMan/DefDAP · GitHub
Skip to content
feat: Add Oxford h5oina support#156

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
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 Merged

rhysgt
merged 5 commits into

from

Aug 24, 2026
 Merged


feat: Add Oxford h5oina support
#156
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6a5ebd1

Add Oxford h5oina support


rhysgt Aug 20, 2026
83e52d4

feat: Add Oxford h5oina support


mikesmic Aug 21, 2026
da9b2e2

feat: Support for processed dataset in h5oina


rhysgt Aug 21, 2026
e8ecfb4

fix: code typo


rhysgt Aug 21, 2026
df899d6

refactor: tidy h5 file reader


mikesmic Aug 21, 2026

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168 changes: 156 additions & 12 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,15 +13,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd
from abc import ABC, abstractmethod
import pathlib
import re

from typing import TextIO, Dict, List, Callable, Any, Type, Optional

import h5py
import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd

from defdap.crystal import Phase
from defdap.quat import Quat
from defdap.utils import Datastore
Expand DownExpand Up@@ -56,11 +57,14 @@ def __init__(self) -> None:
 self.data_format = None

 @staticmethod
 def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]':
 def get_loader(
 data_type: str, file_name: pathlib.Path
 ) -> 'Type[EBSDDataLoader]':
 if data_type is None:
 data_type = {
 '.crc': 'oxfordbinary',
 '.cpr': 'oxfordbinary',
 '.h5oina': 'oxfordh5',
 '.ctf': 'oxfordtext',
 '.ang': 'edaxang',
 }.get(file_name.suffix, 'oxfordbinary')
Expand All@@ -70,6 +74,7 @@ def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]
 loader = {
 'oxfordbinary': OxfordBinaryLoader,
 'oxfordtext': OxfordTextLoader,
 'oxfordh5': Oxfordh5Loader,
 'edaxang': EdaxAngLoader,
 'pythondict': PythonDictLoader,
 }[data_type]
Expand DownExpand Up@@ -234,6 +239,134 @@ def parse_phase() -> Phase:
 self.check_data()


class Oxfordh5Loader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path, dataset = None) -> None:
 """Read an Oxford Instruments ``.h5oina`` orientation file.

 Parameters
 ----------
 file_name : pathlib.Path
 Path to file.
 dataset : str (raw or processed), optional
 Dataset to load. If None, defaults to raw data.

 """
 # Open data file and read in metadata
 if not file_name.is_file():
 raise FileNotFoundError(f"Cannot open file {file_name}")

 file = h5py.File(file_name)

 # This header contains all the information in the map that does not 
 # change with processing
 raw_header = file['1']['EBSD']['Header']
 shape = (int(raw_header['Y Cells'][0]), int(raw_header['X Cells'][0]))
 self.loaded_metadata['shape'] = shape
 self.loaded_metadata['step_size'] = float(raw_header['X Step'][0])
 self.loaded_metadata['acquisition_rotation'] = Quat.from_euler_angles(
 *raw_header['Specimen Orientation Euler'][0]
 )

 # Check if `Data Processing` dataset exists in the h5
 if 'Data' in file['1']['Data Processing'] and dataset is None:
 print('\n\tMultiple datasets in h5 file, defaulting to raw data.')
 print(
 '\tProcessed data can be accessed by passing `processed` to '
 'the `dataset` argument.'
 )

 # Handle `raw` or `processed` selection
 if dataset is None or dataset == 'raw':
 root = file['1']['EBSD']
 if dataset == 'processed':
 if 'Data Processing' not in file['1']:
 raise ValueError('No processed data in h5 file.')
 if 'Data' not in file['1']['Data Processing']:
 raise ValueError('No processed data in h5 file.')
 root = file['1']['Data Processing']

 # Phase data from relevant dataset
 for phase_data in root['Header']['Phases'].values():
 phase = Phase(
 phase_data['Phase Name'][0].decode(),
 phase_data['Laue Group'][0],
 phase_data['Space Group'][0],
 np.concatenate([
 phase_data['Lattice Dimensions'][0],
 phase_data['Lattice Angles'][0]
 ]))
 self.loaded_metadata['phases'].append(phase)

 self.check_metadata()

 # Some data is only available and relevant for the raw data, for 
 # example band contrast
 if dataset == 'raw':
 raw_data = root['Data']
 self.loaded_data.add(
 'band_contrast', 
 np.array(raw_data['Band Contrast']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }
 )
 self.loaded_data.add(
 'band_slope', 
 np.array(raw_data['Band Slope']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band slope',
 }
 )
 self.loaded_data.add(
 'mean_angular_deviation', 
 np.array(raw_data['Mean Angular Deviation']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Mean angular deviation',
 }
 )
 self.loaded_data.add(
 'pattern_quality', 
 np.array(raw_data['Pattern Quality']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Pattern quality',
 }
 )

 # If pattern matching is performed, the cross correlation coefficient 
 # is useful
 if dataset == 'processed' and 'Pattern Matching' in root:
 pattern_data = root['Pattern Matching']['Data']
 self.loaded_data.add(
 'pattern_quality', 
 np.array(
 pattern_data['Cross Correlation Coefficient']
 ).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Cross Correlation Coefficient',
 }
 )

 # Get Euler angles from relevant dataset
 self.loaded_data.phase = np.array(root['Data']['Phase']).reshape(shape)
 self.loaded_data.euler_angle = (
 root['Data']['Euler'][:].reshape(shape + (3,)).transpose((2, 0, 1))
 )

 self.check_data()


class EdaxAngLoader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path) -> None:
 """ Read an EDAX .ang file.
Expand DownExpand Up@@ -327,7 +460,9 @@ def load(self, file_name: pathlib.Path) -> None:
 )
 add_phase = 1 if data['phase'].min() == 0 else 0
 self.loaded_data.phase = data['phase'].reshape(shape) + add_phase
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )

 # flatten the structured dtype
 euler_angle = structured_to_unstructured(
Expand DownExpand Up@@ -424,8 +559,10 @@ def parse_line(line: str, group_dict: Dict) -> None:

 group_name = group_pat.match(line.strip()).group(1)
 group_dict = dict()
 read_until_string(cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict))
 read_until_string(
 cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict)
 )
 metadata[group_name] = group_dict

 # Create phase objects and move metadata to object metadata dict
Expand DownExpand Up@@ -549,7 +686,8 @@ def load_oxford_crc(self, file_name: pathlib.Path) -> None:
 data[['ph1', 'phi', 'ph2']].reshape(shape)).transpose((2, 0, 1))

 if self.loaded_metadata['edx']['Count'] > 0:
 EDXFields = [key for key in data.dtype.fields.keys() if key.startswith('EDX')]
 EDXFields = [key for key in data.dtype.fields.keys() 
 if key.startswith('EDX')]
 for field in EDXFields:
 self.loaded_data.add(
 field,
Expand DownExpand Up@@ -590,7 +728,9 @@ def load(self, data_dict: Dict[str, Any]) -> None:
 unit='', type='map', order=0
 )
 self.loaded_data.phase = data_dict['phase']
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )
 self.loaded_data.euler_angle = data_dict['euler_angle']
 self.check_data()

Expand DownExpand Up@@ -819,8 +959,12 @@ def load(self, file_name: pathlib.Path) -> None:

 # if y descending, flip
 if np.all(np.diff(data['y'][:,0])) > 0:
 self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
 self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
 self.loaded_data.coordinate = np.array(
 [data['x'][::-1], data['y'][::-1]]
 )
 self.loaded_data.displacement = np.array(
 [data['u'][::-1], data['v'][::-1]]
 )
 else:
 self.loaded_data.coordinate = np.array([data['x'], data['y']])
 self.loaded_data.displacement = np.array([data['u'], data['v']])
Expand Down

1 change: 1 addition & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -41,6 +41,7 @@ dependencies = [
 "matplotlib_scalebar",
 "networkx",
 "numba",
 "h5py"
]

[project.urls]
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
feat: Add Oxford h5oina support by rhysgt · Pull Request #156 · MechMicroMan/DefDAP · GitHub
Skip to content
feat: Add Oxford h5oina support#156

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 Merged

rhysgt
merged 5 commits into

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Aug 24, 2026
 Merged


feat: Add Oxford h5oina support
#156
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6a5ebd1

Add Oxford h5oina support


rhysgt Aug 20, 2026
83e52d4

feat: Add Oxford h5oina support


mikesmic Aug 21, 2026
da9b2e2

feat: Support for processed dataset in h5oina


rhysgt Aug 21, 2026
e8ecfb4

fix: code typo


rhysgt Aug 21, 2026
df899d6

refactor: tidy h5 file reader


mikesmic Aug 21, 2026

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168 changes: 156 additions & 12 deletions
defdap/file_readers.py

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -13,15 +13,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd
from abc import ABC, abstractmethod
import pathlib
import re

from typing import TextIO, Dict, List, Callable, Any, Type, Optional

import h5py
import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd

from defdap.crystal import Phase
from defdap.quat import Quat
from defdap.utils import Datastore
Expand DownExpand Up@@ -56,11 +57,14 @@ def __init__(self) -> None:
 self.data_format = None

 @staticmethod
 def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]':
 def get_loader(
 data_type: str, file_name: pathlib.Path
 ) -> 'Type[EBSDDataLoader]':
 if data_type is None:
 data_type = {
 '.crc': 'oxfordbinary',
 '.cpr': 'oxfordbinary',
 '.h5oina': 'oxfordh5',
 '.ctf': 'oxfordtext',
 '.ang': 'edaxang',
 }.get(file_name.suffix, 'oxfordbinary')
Expand All@@ -70,6 +74,7 @@ def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]
 loader = {
 'oxfordbinary': OxfordBinaryLoader,
 'oxfordtext': OxfordTextLoader,
 'oxfordh5': Oxfordh5Loader,
 'edaxang': EdaxAngLoader,
 'pythondict': PythonDictLoader,
 }[data_type]
Expand DownExpand Up@@ -234,6 +239,134 @@ def parse_phase() -> Phase:
 self.check_data()


class Oxfordh5Loader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path, dataset = None) -> None:
 """Read an Oxford Instruments ``.h5oina`` orientation file.

 Parameters
 ----------
 file_name : pathlib.Path
 Path to file.
 dataset : str (raw or processed), optional
 Dataset to load. If None, defaults to raw data.

 """
 # Open data file and read in metadata
 if not file_name.is_file():
 raise FileNotFoundError(f"Cannot open file {file_name}")

 file = h5py.File(file_name)

 # This header contains all the information in the map that does not 
 # change with processing
 raw_header = file['1']['EBSD']['Header']
 shape = (int(raw_header['Y Cells'][0]), int(raw_header['X Cells'][0]))
 self.loaded_metadata['shape'] = shape
 self.loaded_metadata['step_size'] = float(raw_header['X Step'][0])
 self.loaded_metadata['acquisition_rotation'] = Quat.from_euler_angles(
 *raw_header['Specimen Orientation Euler'][0]
 )

 # Check if `Data Processing` dataset exists in the h5
 if 'Data' in file['1']['Data Processing'] and dataset is None:
 print('\n\tMultiple datasets in h5 file, defaulting to raw data.')
 print(
 '\tProcessed data can be accessed by passing `processed` to '
 'the `dataset` argument.'
 )

 # Handle `raw` or `processed` selection
 if dataset is None or dataset == 'raw':
 root = file['1']['EBSD']
 if dataset == 'processed':
 if 'Data Processing' not in file['1']:
 raise ValueError('No processed data in h5 file.')
 if 'Data' not in file['1']['Data Processing']:
 raise ValueError('No processed data in h5 file.')
 root = file['1']['Data Processing']

 # Phase data from relevant dataset
 for phase_data in root['Header']['Phases'].values():
 phase = Phase(
 phase_data['Phase Name'][0].decode(),
 phase_data['Laue Group'][0],
 phase_data['Space Group'][0],
 np.concatenate([
 phase_data['Lattice Dimensions'][0],
 phase_data['Lattice Angles'][0]
 ]))
 self.loaded_metadata['phases'].append(phase)

 self.check_metadata()

 # Some data is only available and relevant for the raw data, for 
 # example band contrast
 if dataset == 'raw':
 raw_data = root['Data']
 self.loaded_data.add(
 'band_contrast', 
 np.array(raw_data['Band Contrast']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }
 )
 self.loaded_data.add(
 'band_slope', 
 np.array(raw_data['Band Slope']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band slope',
 }
 )
 self.loaded_data.add(
 'mean_angular_deviation', 
 np.array(raw_data['Mean Angular Deviation']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Mean angular deviation',
 }
 )
 self.loaded_data.add(
 'pattern_quality', 
 np.array(raw_data['Pattern Quality']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Pattern quality',
 }
 )

 # If pattern matching is performed, the cross correlation coefficient 
 # is useful
 if dataset == 'processed' and 'Pattern Matching' in root:
 pattern_data = root['Pattern Matching']['Data']
 self.loaded_data.add(
 'pattern_quality', 
 np.array(
 pattern_data['Cross Correlation Coefficient']
 ).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Cross Correlation Coefficient',
 }
 )

 # Get Euler angles from relevant dataset
 self.loaded_data.phase = np.array(root['Data']['Phase']).reshape(shape)
 self.loaded_data.euler_angle = (
 root['Data']['Euler'][:].reshape(shape + (3,)).transpose((2, 0, 1))
 )

 self.check_data()


class EdaxAngLoader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path) -> None:
 """ Read an EDAX .ang file.
Expand DownExpand Up@@ -327,7 +460,9 @@ def load(self, file_name: pathlib.Path) -> None:
 )
 add_phase = 1 if data['phase'].min() == 0 else 0
 self.loaded_data.phase = data['phase'].reshape(shape) + add_phase
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )

 # flatten the structured dtype
 euler_angle = structured_to_unstructured(
Expand DownExpand Up@@ -424,8 +559,10 @@ def parse_line(line: str, group_dict: Dict) -> None:

 group_name = group_pat.match(line.strip()).group(1)
 group_dict = dict()
 read_until_string(cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict))
 read_until_string(
 cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict)
 )
 metadata[group_name] = group_dict

 # Create phase objects and move metadata to object metadata dict
Expand DownExpand Up@@ -549,7 +686,8 @@ def load_oxford_crc(self, file_name: pathlib.Path) -> None:
 data[['ph1', 'phi', 'ph2']].reshape(shape)).transpose((2, 0, 1))

 if self.loaded_metadata['edx']['Count'] > 0:
 EDXFields = [key for key in data.dtype.fields.keys() if key.startswith('EDX')]
 EDXFields = [key for key in data.dtype.fields.keys() 
 if key.startswith('EDX')]
 for field in EDXFields:
 self.loaded_data.add(
 field,
Expand DownExpand Up@@ -590,7 +728,9 @@ def load(self, data_dict: Dict[str, Any]) -> None:
 unit='', type='map', order=0
 )
 self.loaded_data.phase = data_dict['phase']
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )
 self.loaded_data.euler_angle = data_dict['euler_angle']
 self.check_data()

Expand DownExpand Up@@ -819,8 +959,12 @@ def load(self, file_name: pathlib.Path) -> None:

 # if y descending, flip
 if np.all(np.diff(data['y'][:,0])) > 0:
 self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
 self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
 self.loaded_data.coordinate = np.array(
 [data['x'][::-1], data['y'][::-1]]
 )
 self.loaded_data.displacement = np.array(
 [data['u'][::-1], data['v'][::-1]]
 )
 else:
 self.loaded_data.coordinate = np.array([data['x'], data['y']])
 self.loaded_data.displacement = np.array([data['u'], data['v']])
Expand Down

1 change: 1 addition & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -41,6 +41,7 @@ dependencies = [
 "matplotlib_scalebar",
 "networkx",
 "numba",
 "h5py"
]

[project.urls]
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
feat: Add Oxford h5oina support by rhysgt · Pull Request #156 · MechMicroMan/DefDAP · GitHub
Skip to content
feat: Add Oxford h5oina support#156

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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 Merged

rhysgt
merged 5 commits into

from

Aug 24, 2026
 Merged


feat: Add Oxford h5oina support
#156
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6a5ebd1

Add Oxford h5oina support


rhysgt Aug 20, 2026
83e52d4

feat: Add Oxford h5oina support


mikesmic Aug 21, 2026
da9b2e2

feat: Support for processed dataset in h5oina


rhysgt Aug 21, 2026
e8ecfb4

fix: code typo


rhysgt Aug 21, 2026
df899d6

refactor: tidy h5 file reader


mikesmic Aug 21, 2026

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168 changes: 156 additions & 12 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,15 +13,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd
from abc import ABC, abstractmethod
import pathlib
import re

from typing import TextIO, Dict, List, Callable, Any, Type, Optional

import h5py
import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd

from defdap.crystal import Phase
from defdap.quat import Quat
from defdap.utils import Datastore
Expand DownExpand Up@@ -56,11 +57,14 @@ def __init__(self) -> None:
 self.data_format = None

 @staticmethod
 def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]':
 def get_loader(
 data_type: str, file_name: pathlib.Path
 ) -> 'Type[EBSDDataLoader]':
 if data_type is None:
 data_type = {
 '.crc': 'oxfordbinary',
 '.cpr': 'oxfordbinary',
 '.h5oina': 'oxfordh5',
 '.ctf': 'oxfordtext',
 '.ang': 'edaxang',
 }.get(file_name.suffix, 'oxfordbinary')
Expand All@@ -70,6 +74,7 @@ def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]
 loader = {
 'oxfordbinary': OxfordBinaryLoader,
 'oxfordtext': OxfordTextLoader,
 'oxfordh5': Oxfordh5Loader,
 'edaxang': EdaxAngLoader,
 'pythondict': PythonDictLoader,
 }[data_type]
Expand DownExpand Up@@ -234,6 +239,134 @@ def parse_phase() -> Phase:
 self.check_data()


class Oxfordh5Loader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path, dataset = None) -> None:
 """Read an Oxford Instruments ``.h5oina`` orientation file.

 Parameters
 ----------
 file_name : pathlib.Path
 Path to file.
 dataset : str (raw or processed), optional
 Dataset to load. If None, defaults to raw data.

 """
 # Open data file and read in metadata
 if not file_name.is_file():
 raise FileNotFoundError(f"Cannot open file {file_name}")

 file = h5py.File(file_name)

 # This header contains all the information in the map that does not 
 # change with processing
 raw_header = file['1']['EBSD']['Header']
 shape = (int(raw_header['Y Cells'][0]), int(raw_header['X Cells'][0]))
 self.loaded_metadata['shape'] = shape
 self.loaded_metadata['step_size'] = float(raw_header['X Step'][0])
 self.loaded_metadata['acquisition_rotation'] = Quat.from_euler_angles(
 *raw_header['Specimen Orientation Euler'][0]
 )

 # Check if `Data Processing` dataset exists in the h5
 if 'Data' in file['1']['Data Processing'] and dataset is None:
 print('\n\tMultiple datasets in h5 file, defaulting to raw data.')
 print(
 '\tProcessed data can be accessed by passing `processed` to '
 'the `dataset` argument.'
 )

 # Handle `raw` or `processed` selection
 if dataset is None or dataset == 'raw':
 root = file['1']['EBSD']
 if dataset == 'processed':
 if 'Data Processing' not in file['1']:
 raise ValueError('No processed data in h5 file.')
 if 'Data' not in file['1']['Data Processing']:
 raise ValueError('No processed data in h5 file.')
 root = file['1']['Data Processing']

 # Phase data from relevant dataset
 for phase_data in root['Header']['Phases'].values():
 phase = Phase(
 phase_data['Phase Name'][0].decode(),
 phase_data['Laue Group'][0],
 phase_data['Space Group'][0],
 np.concatenate([
 phase_data['Lattice Dimensions'][0],
 phase_data['Lattice Angles'][0]
 ]))
 self.loaded_metadata['phases'].append(phase)

 self.check_metadata()

 # Some data is only available and relevant for the raw data, for 
 # example band contrast
 if dataset == 'raw':
 raw_data = root['Data']
 self.loaded_data.add(
 'band_contrast', 
 np.array(raw_data['Band Contrast']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }
 )
 self.loaded_data.add(
 'band_slope', 
 np.array(raw_data['Band Slope']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band slope',
 }
 )
 self.loaded_data.add(
 'mean_angular_deviation', 
 np.array(raw_data['Mean Angular Deviation']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Mean angular deviation',
 }
 )
 self.loaded_data.add(
 'pattern_quality', 
 np.array(raw_data['Pattern Quality']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Pattern quality',
 }
 )

 # If pattern matching is performed, the cross correlation coefficient 
 # is useful
 if dataset == 'processed' and 'Pattern Matching' in root:
 pattern_data = root['Pattern Matching']['Data']
 self.loaded_data.add(
 'pattern_quality', 
 np.array(
 pattern_data['Cross Correlation Coefficient']
 ).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Cross Correlation Coefficient',
 }
 )

 # Get Euler angles from relevant dataset
 self.loaded_data.phase = np.array(root['Data']['Phase']).reshape(shape)
 self.loaded_data.euler_angle = (
 root['Data']['Euler'][:].reshape(shape + (3,)).transpose((2, 0, 1))
 )

 self.check_data()


class EdaxAngLoader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path) -> None:
 """ Read an EDAX .ang file.
Expand DownExpand Up@@ -327,7 +460,9 @@ def load(self, file_name: pathlib.Path) -> None:
 )
 add_phase = 1 if data['phase'].min() == 0 else 0
 self.loaded_data.phase = data['phase'].reshape(shape) + add_phase
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )

 # flatten the structured dtype
 euler_angle = structured_to_unstructured(
Expand DownExpand Up@@ -424,8 +559,10 @@ def parse_line(line: str, group_dict: Dict) -> None:

 group_name = group_pat.match(line.strip()).group(1)
 group_dict = dict()
 read_until_string(cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict))
 read_until_string(
 cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict)
 )
 metadata[group_name] = group_dict

 # Create phase objects and move metadata to object metadata dict
Expand DownExpand Up@@ -549,7 +686,8 @@ def load_oxford_crc(self, file_name: pathlib.Path) -> None:
 data[['ph1', 'phi', 'ph2']].reshape(shape)).transpose((2, 0, 1))

 if self.loaded_metadata['edx']['Count'] > 0:
 EDXFields = [key for key in data.dtype.fields.keys() if key.startswith('EDX')]
 EDXFields = [key for key in data.dtype.fields.keys() 
 if key.startswith('EDX')]
 for field in EDXFields:
 self.loaded_data.add(
 field,
Expand DownExpand Up@@ -590,7 +728,9 @@ def load(self, data_dict: Dict[str, Any]) -> None:
 unit='', type='map', order=0
 )
 self.loaded_data.phase = data_dict['phase']
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )
 self.loaded_data.euler_angle = data_dict['euler_angle']
 self.check_data()

Expand DownExpand Up@@ -819,8 +959,12 @@ def load(self, file_name: pathlib.Path) -> None:

 # if y descending, flip
 if np.all(np.diff(data['y'][:,0])) > 0:
 self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
 self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
 self.loaded_data.coordinate = np.array(
 [data['x'][::-1], data['y'][::-1]]
 )
 self.loaded_data.displacement = np.array(
 [data['u'][::-1], data['v'][::-1]]
 )
 else:
 self.loaded_data.coordinate = np.array([data['x'], data['y']])
 self.loaded_data.displacement = np.array([data['u'], data['v']])
Expand Down

1 change: 1 addition & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -41,6 +41,7 @@ dependencies = [
 "matplotlib_scalebar",
 "networkx",
 "numba",
 "h5py"
]

[project.urls]
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
feat: Add Oxford h5oina support by rhysgt · Pull Request #156 · MechMicroMan/DefDAP · GitHub
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 Merged

rhysgt
merged 5 commits into

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Aug 24, 2026
 Merged


feat: Add Oxford h5oina support
#156
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6a5ebd1

Add Oxford h5oina support


rhysgt Aug 20, 2026
83e52d4

feat: Add Oxford h5oina support


mikesmic Aug 21, 2026
da9b2e2

feat: Support for processed dataset in h5oina


rhysgt Aug 21, 2026
e8ecfb4

fix: code typo


rhysgt Aug 21, 2026
df899d6

refactor: tidy h5 file reader


mikesmic Aug 21, 2026

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168 changes: 156 additions & 12 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,15 +13,16 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd
from abc import ABC, abstractmethod
import pathlib
import re

from typing import TextIO, Dict, List, Callable, Any, Type, Optional

import h5py
import numpy as np
from numpy.lib.recfunctions import structured_to_unstructured
import pandas as pd

from defdap.crystal import Phase
from defdap.quat import Quat
from defdap.utils import Datastore
Expand DownExpand Up@@ -56,11 +57,14 @@ def __init__(self) -> None:
 self.data_format = None

 @staticmethod
 def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]':
 def get_loader(
 data_type: str, file_name: pathlib.Path
 ) -> 'Type[EBSDDataLoader]':
 if data_type is None:
 data_type = {
 '.crc': 'oxfordbinary',
 '.cpr': 'oxfordbinary',
 '.h5oina': 'oxfordh5',
 '.ctf': 'oxfordtext',
 '.ang': 'edaxang',
 }.get(file_name.suffix, 'oxfordbinary')
Expand All@@ -70,6 +74,7 @@ def get_loader(data_type: str, file_name: pathlib.Path) -> 'Type[EBSDDataLoader]
 loader = {
 'oxfordbinary': OxfordBinaryLoader,
 'oxfordtext': OxfordTextLoader,
 'oxfordh5': Oxfordh5Loader,
 'edaxang': EdaxAngLoader,
 'pythondict': PythonDictLoader,
 }[data_type]
Expand DownExpand Up@@ -234,6 +239,134 @@ def parse_phase() -> Phase:
 self.check_data()


class Oxfordh5Loader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path, dataset = None) -> None:
 """Read an Oxford Instruments ``.h5oina`` orientation file.

 Parameters
 ----------
 file_name : pathlib.Path
 Path to file.
 dataset : str (raw or processed), optional
 Dataset to load. If None, defaults to raw data.

 """
 # Open data file and read in metadata
 if not file_name.is_file():
 raise FileNotFoundError(f"Cannot open file {file_name}")

 file = h5py.File(file_name)

 # This header contains all the information in the map that does not 
 # change with processing
 raw_header = file['1']['EBSD']['Header']
 shape = (int(raw_header['Y Cells'][0]), int(raw_header['X Cells'][0]))
 self.loaded_metadata['shape'] = shape
 self.loaded_metadata['step_size'] = float(raw_header['X Step'][0])
 self.loaded_metadata['acquisition_rotation'] = Quat.from_euler_angles(
 *raw_header['Specimen Orientation Euler'][0]
 )

 # Check if `Data Processing` dataset exists in the h5
 if 'Data' in file['1']['Data Processing'] and dataset is None:
 print('\n\tMultiple datasets in h5 file, defaulting to raw data.')
 print(
 '\tProcessed data can be accessed by passing `processed` to '
 'the `dataset` argument.'
 )

 # Handle `raw` or `processed` selection
 if dataset is None or dataset == 'raw':
 root = file['1']['EBSD']
 if dataset == 'processed':
 if 'Data Processing' not in file['1']:
 raise ValueError('No processed data in h5 file.')
 if 'Data' not in file['1']['Data Processing']:
 raise ValueError('No processed data in h5 file.')
 root = file['1']['Data Processing']

 # Phase data from relevant dataset
 for phase_data in root['Header']['Phases'].values():
 phase = Phase(
 phase_data['Phase Name'][0].decode(),
 phase_data['Laue Group'][0],
 phase_data['Space Group'][0],
 np.concatenate([
 phase_data['Lattice Dimensions'][0],
 phase_data['Lattice Angles'][0]
 ]))
 self.loaded_metadata['phases'].append(phase)

 self.check_metadata()

 # Some data is only available and relevant for the raw data, for 
 # example band contrast
 if dataset == 'raw':
 raw_data = root['Data']
 self.loaded_data.add(
 'band_contrast', 
 np.array(raw_data['Band Contrast']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }
 )
 self.loaded_data.add(
 'band_slope', 
 np.array(raw_data['Band Slope']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'cmap': 'gray',
 'clabel': 'Band slope',
 }
 )
 self.loaded_data.add(
 'mean_angular_deviation', 
 np.array(raw_data['Mean Angular Deviation']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Mean angular deviation',
 }
 )
 self.loaded_data.add(
 'pattern_quality', 
 np.array(raw_data['Pattern Quality']).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Pattern quality',
 }
 )

 # If pattern matching is performed, the cross correlation coefficient 
 # is useful
 if dataset == 'processed' and 'Pattern Matching' in root:
 pattern_data = root['Pattern Matching']['Data']
 self.loaded_data.add(
 'pattern_quality', 
 np.array(
 pattern_data['Cross Correlation Coefficient']
 ).reshape(shape),
 unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': True,
 'clabel': 'Cross Correlation Coefficient',
 }
 )

 # Get Euler angles from relevant dataset
 self.loaded_data.phase = np.array(root['Data']['Phase']).reshape(shape)
 self.loaded_data.euler_angle = (
 root['Data']['Euler'][:].reshape(shape + (3,)).transpose((2, 0, 1))
 )

 self.check_data()


class EdaxAngLoader(EBSDDataLoader):
 def load(self, file_name: pathlib.Path) -> None:
 """ Read an EDAX .ang file.
Expand DownExpand Up@@ -327,7 +460,9 @@ def load(self, file_name: pathlib.Path) -> None:
 )
 add_phase = 1 if data['phase'].min() == 0 else 0
 self.loaded_data.phase = data['phase'].reshape(shape) + add_phase
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )

 # flatten the structured dtype
 euler_angle = structured_to_unstructured(
Expand DownExpand Up@@ -424,8 +559,10 @@ def parse_line(line: str, group_dict: Dict) -> None:

 group_name = group_pat.match(line.strip()).group(1)
 group_dict = dict()
 read_until_string(cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict))
 read_until_string(
 cpr_file, '[', comment_char=comment_char,
 line_process=lambda l: parse_line(l, group_dict)
 )
 metadata[group_name] = group_dict

 # Create phase objects and move metadata to object metadata dict
Expand DownExpand Up@@ -549,7 +686,8 @@ def load_oxford_crc(self, file_name: pathlib.Path) -> None:
 data[['ph1', 'phi', 'ph2']].reshape(shape)).transpose((2, 0, 1))

 if self.loaded_metadata['edx']['Count'] > 0:
 EDXFields = [key for key in data.dtype.fields.keys() if key.startswith('EDX')]
 EDXFields = [key for key in data.dtype.fields.keys() 
 if key.startswith('EDX')]
 for field in EDXFields:
 self.loaded_data.add(
 field,
Expand DownExpand Up@@ -590,7 +728,9 @@ def load(self, data_dict: Dict[str, Any]) -> None:
 unit='', type='map', order=0
 )
 self.loaded_data.phase = data_dict['phase']
 self.loaded_data['phase', 'plot_params']['vmax'] = len(self.loaded_metadata['phases'])
 self.loaded_data['phase', 'plot_params']['vmax'] = len(
 self.loaded_metadata['phases']
 )
 self.loaded_data.euler_angle = data_dict['euler_angle']
 self.check_data()

Expand DownExpand Up@@ -819,8 +959,12 @@ def load(self, file_name: pathlib.Path) -> None:

 # if y descending, flip
 if np.all(np.diff(data['y'][:,0])) > 0:
 self.loaded_data.coordinate = np.array([data['x'][::-1], data['y'][::-1]])
 self.loaded_data.displacement = np.array([data['u'][::-1], data['v'][::-1]])
 self.loaded_data.coordinate = np.array(
 [data['x'][::-1], data['y'][::-1]]
 )
 self.loaded_data.displacement = np.array(
 [data['u'][::-1], data['v'][::-1]]
 )
 else:
 self.loaded_data.coordinate = np.array([data['x'], data['y']])
 self.loaded_data.displacement = np.array([data['u'], data['v']])
Expand Down

1 change: 1 addition & 0 deletions
pyproject.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -41,6 +41,7 @@ dependencies = [
 "matplotlib_scalebar",
 "networkx",
 "numba",
 "h5py"
]

[project.urls]
Expand Down
Loading