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Adding a class for images #133

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97ab620
Added optical class with import functions
Sep 29, 2024
b5452d4
Worked until add_homog_points
Oct 2, 2024
a1bce2b
Updates to optical image class
mikesmic Oct 15, 2024
3979d33
Initial commit
Nov 13, 2024
3970507
alltrue depreceated
rhysgt Nov 20, 2024
1bd2a4f
Fix unit cell plotting
rhysgt Nov 21, 2024
cb1ffd2
Combine optical and hrdic grain inspectors
rhysgt Nov 21, 2024
0794327
Update copyright year
rhysgt Nov 21, 2024
15f873b
Remove reference to DIC
rhysgt Nov 21, 2024
6b33a60
Tidy example optical notebook
rhysgt Nov 21, 2024
b6cfe6d
Update optical.ipynb
rhysgt Nov 21, 2024
3f4c4d1
Implement mixin class for hrdic/optical
rhysgt Dec 8, 2024
16ee030
Generalise rotate_data for 90, 180, 270 degree rotations
rhysgt Dec 8, 2024
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3 changes: 2 additions & 1 deletion defdap/base.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -921,6 +921,7 @@ def grain_data(self, map_data):

return grain_data


def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
"""Extract a single grain map from the given map data.

Expand Down
2 changes: 1 addition & 1 deletion defdap/crystal.py
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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down
41 changes: 27 additions & 14 deletions defdap/ebsd.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -242,21 +242,34 @@ def scale(self):
return self.step_size

@report_progress("rotating EBSD data")
def rotate_data(self):
"""Rotate map by 180 degrees and transform quats accordingly.
def rotate_data(self, angle=180):
"""Rotate map counter-clockwise by the specified angle (90, 180, 270 degrees)
and transform quats accordingly.

"""

self.data.euler_angle = self.data.euler_angle[:, ::-1, ::-1]
self.data.band_contrast = self.data.band_contrast[::-1, ::-1]
self.data.band_slope = self.data.band_slope[::-1, ::-1]
self.data.phase = self.data.phase[::-1, ::-1]
self.calc_quat_array()

# Rotation from old coord system to new
transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.pi).conjugate
Parameters
----------
angle : int
The angle to rotate the map. Must be one of [90, 180, 270].

# Perform vectorised multiplication
"""
if angle not in [90, 180, 270]:
raise ValueError("Angle must be one of [90, 180, 270]")

# Rotate the data arrays by the specified angle
k = angle // 90 # Number of 90 degree rotations

# Change the shape of the EBSD data to match
if k % 2 == 1:
self.shape = self.shape[::-1]

self.data.euler_angle = np.rot90(self.data.euler_angle, k=k, axes=(1, 2))
self.data.band_contrast = np.rot90(self.data.band_contrast, k=k)
self.data.mean_angular_deviation = np.rot90(self.data.mean_angular_deviation, k=k)
self.data.band_slope = np.rot90(self.data.band_slope, k=k)
self.data.phase = np.rot90(self.data.phase, k=k)

# Rotation quaterions from old coord system to new
transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.deg2rad(-angle)).conjugate
quats = Quat.multiply_many_quats(self.data.orientation.flatten(), transform_quat)
self.data.orientation = np.array(quats).reshape(self.shape)

Expand Down
22 changes: 20 additions & 2 deletions defdap/file_readers.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand All@@ -19,6 +19,7 @@
from abc import ABC, abstractmethod
import pathlib
import re
from skimage.io import imread

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

Expand DownExpand Up@@ -205,7 +206,6 @@ def parse_phase() -> Phase:
'cmap': 'gray',
'clabel': 'Band contrast',
}

)
self.loaded_data.add(
'band_slope', data['BS'].reshape(shape),
Expand DownExpand Up@@ -791,13 +791,31 @@ def load(self, file_name: pathlib.Path) -> None:
self.check_data()


def load_image(file_name: pathlib.Path) -> Datastore:
image = imread(file_name, as_gray=True)
loaded_metadata = {
'shape': image.shape,
}
laoded_data = Datastore()
laoded_data.add(
'image', image, unit='', type='map', order=0,
plot_params={
'plot_colour_bar': False,
'cmap': 'gray',
}
)
return loaded_metadata, laoded_data


def read_until_string(
file: TextIO,
term_string: str,
comment_char: str = '*',
line_process: Optional[Callable[[str], Any]] = None,
exact: bool = False
) -> List[Any]:


"""Read lines in a file until a line starting with the `termString`
is encountered. The file position is returned before the line starting
with the `termString` when found. Comment and empty lines are ignored.
Expand Down
2 changes: 1 addition & 1 deletion defdap/file_writers.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
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" + '
Adding a class for images by rhysgt · Pull Request #133 · MechMicroMan/DefDAP · GitHub
Skip to content
Adding a class for images#133

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to your account

 Open

rhysgt
wants to merge
13
commits into

base:develop
Choose a base branch

from

 Open


Adding a class for images
#133
Show file tree
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13 commits


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Hold shift + click to select a range
97ab620

Added optical class with import functions

Sep 29, 2024
b5452d4

Worked until add_homog_points

Oct 2, 2024
a1bce2b

Updates to optical image class


mikesmic Oct 15, 2024
3979d33

Initial commit

Nov 13, 2024
3970507

alltrue depreceated


rhysgt Nov 20, 2024
1bd2a4f

Fix unit cell plotting


rhysgt Nov 21, 2024
cb1ffd2

Combine optical and hrdic grain inspectors


rhysgt Nov 21, 2024
0794327

Update copyright year


rhysgt Nov 21, 2024
15f873b

Remove reference to DIC


rhysgt Nov 21, 2024
6b33a60

Tidy example optical notebook


rhysgt Nov 21, 2024
b6cfe6d

Update optical.ipynb


rhysgt Nov 21, 2024
3f4c4d1

Implement mixin class for hrdic/optical


rhysgt Dec 8, 2024
16ee030

Generalise rotate_data for 90, 180, 270 degree rotations


rhysgt Dec 8, 2024

File filter

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3 changes: 2 additions & 1 deletion
defdap/base.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -921,6 +921,7 @@ def grain_data(self, map_data):

 return grain_data


 def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
 """Extract a single grain map from the given map data.

Expand Down

2 changes: 1 addition & 1 deletion
defdap/crystal.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down

41 changes: 27 additions & 14 deletions
defdap/ebsd.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -242,21 +242,34 @@ def scale(self):
 return self.step_size

 @report_progress("rotating EBSD data")
 def rotate_data(self):
 """Rotate map by 180 degrees and transform quats accordingly.
 def rotate_data(self, angle=180):
 """Rotate map counter-clockwise by the specified angle (90, 180, 270 degrees) 
 and transform quats accordingly.

 """

 self.data.euler_angle = self.data.euler_angle[:, ::-1, ::-1]
 self.data.band_contrast = self.data.band_contrast[::-1, ::-1]
 self.data.band_slope = self.data.band_slope[::-1, ::-1]
 self.data.phase = self.data.phase[::-1, ::-1]
 self.calc_quat_array()

 # Rotation from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.pi).conjugate
 Parameters
 ----------
 angle : int
 The angle to rotate the map. Must be one of [90, 180, 270].

 # Perform vectorised multiplication
 """
 if angle not in [90, 180, 270]:
 raise ValueError("Angle must be one of [90, 180, 270]")

 # Rotate the data arrays by the specified angle
 k = angle // 90 # Number of 90 degree rotations

 # Change the shape of the EBSD data to match
 if k % 2 == 1:
 self.shape = self.shape[::-1]

 self.data.euler_angle = np.rot90(self.data.euler_angle, k=k, axes=(1, 2))
 self.data.band_contrast = np.rot90(self.data.band_contrast, k=k)
 self.data.mean_angular_deviation = np.rot90(self.data.mean_angular_deviation, k=k)
 self.data.band_slope = np.rot90(self.data.band_slope, k=k)
 self.data.phase = np.rot90(self.data.phase, k=k)

 # Rotation quaterions from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.deg2rad(-angle)).conjugate
 quats = Quat.multiply_many_quats(self.data.orientation.flatten(), transform_quat)
 self.data.orientation = np.array(quats).reshape(self.shape)

Expand Down

22 changes: 20 additions & 2 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand All@@ -19,6 +19,7 @@
from abc import ABC, abstractmethod
import pathlib
import re
from skimage.io import imread

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

Expand DownExpand Up@@ -205,7 +206,6 @@ def parse_phase() -> Phase:
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }

 )
 self.loaded_data.add(
 'band_slope', data['BS'].reshape(shape),
Expand DownExpand Up@@ -791,13 +791,31 @@ def load(self, file_name: pathlib.Path) -> None:
 self.check_data()


def load_image(file_name: pathlib.Path) -> Datastore:
 image = imread(file_name, as_gray=True)
 loaded_metadata = {
 'shape': image.shape,
 }
 laoded_data = Datastore()
 laoded_data.add(
 'image', image, unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': False,
 'cmap': 'gray',
 }
 )
 return loaded_metadata, laoded_data


def read_until_string(
 file: TextIO,
 term_string: str,
 comment_char: str = '*',
 line_process: Optional[Callable[[str], Any]] = None,
 exact: bool = False
) -> List[Any]:


 """Read lines in a file until a line starting with the `termString`
 is encountered. The file position is returned before the line starting
 with the `termString` when found. Comment and empty lines are ignored.
Expand Down

2 changes: 1 addition & 1 deletion
defdap/file_writers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
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; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Adding a class for images by rhysgt · Pull Request #133 · MechMicroMan/DefDAP · GitHub
Skip to content
Adding a class for images#133

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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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to your account

 Open

rhysgt
wants to merge
13
commits into

base:develop
Choose a base branch

from

 Open


Adding a class for images
#133
Show file tree
Hide file tree
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Commits

Show all changes


13 commits


Select commit
Hold shift + click to select a range
97ab620

Added optical class with import functions

Sep 29, 2024
b5452d4

Worked until add_homog_points

Oct 2, 2024
a1bce2b

Updates to optical image class


mikesmic Oct 15, 2024
3979d33

Initial commit

Nov 13, 2024
3970507

alltrue depreceated


rhysgt Nov 20, 2024
1bd2a4f

Fix unit cell plotting


rhysgt Nov 21, 2024
cb1ffd2

Combine optical and hrdic grain inspectors


rhysgt Nov 21, 2024
0794327

Update copyright year


rhysgt Nov 21, 2024
15f873b

Remove reference to DIC


rhysgt Nov 21, 2024
6b33a60

Tidy example optical notebook


rhysgt Nov 21, 2024
b6cfe6d

Update optical.ipynb


rhysgt Nov 21, 2024
3f4c4d1

Implement mixin class for hrdic/optical


rhysgt Dec 8, 2024
16ee030

Generalise rotate_data for 90, 180, 270 degree rotations


rhysgt Dec 8, 2024

File filter

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Filter by extension
Conversations

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Loading
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3 changes: 2 additions & 1 deletion
defdap/base.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -921,6 +921,7 @@ def grain_data(self, map_data):

 return grain_data


 def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
 """Extract a single grain map from the given map data.

Expand Down

2 changes: 1 addition & 1 deletion
defdap/crystal.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down

41 changes: 27 additions & 14 deletions
defdap/ebsd.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -242,21 +242,34 @@ def scale(self):
 return self.step_size

 @report_progress("rotating EBSD data")
 def rotate_data(self):
 """Rotate map by 180 degrees and transform quats accordingly.
 def rotate_data(self, angle=180):
 """Rotate map counter-clockwise by the specified angle (90, 180, 270 degrees) 
 and transform quats accordingly.

 """

 self.data.euler_angle = self.data.euler_angle[:, ::-1, ::-1]
 self.data.band_contrast = self.data.band_contrast[::-1, ::-1]
 self.data.band_slope = self.data.band_slope[::-1, ::-1]
 self.data.phase = self.data.phase[::-1, ::-1]
 self.calc_quat_array()

 # Rotation from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.pi).conjugate
 Parameters
 ----------
 angle : int
 The angle to rotate the map. Must be one of [90, 180, 270].

 # Perform vectorised multiplication
 """
 if angle not in [90, 180, 270]:
 raise ValueError("Angle must be one of [90, 180, 270]")

 # Rotate the data arrays by the specified angle
 k = angle // 90 # Number of 90 degree rotations

 # Change the shape of the EBSD data to match
 if k % 2 == 1:
 self.shape = self.shape[::-1]

 self.data.euler_angle = np.rot90(self.data.euler_angle, k=k, axes=(1, 2))
 self.data.band_contrast = np.rot90(self.data.band_contrast, k=k)
 self.data.mean_angular_deviation = np.rot90(self.data.mean_angular_deviation, k=k)
 self.data.band_slope = np.rot90(self.data.band_slope, k=k)
 self.data.phase = np.rot90(self.data.phase, k=k)

 # Rotation quaterions from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.deg2rad(-angle)).conjugate
 quats = Quat.multiply_many_quats(self.data.orientation.flatten(), transform_quat)
 self.data.orientation = np.array(quats).reshape(self.shape)

Expand Down

22 changes: 20 additions & 2 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand All@@ -19,6 +19,7 @@
from abc import ABC, abstractmethod
import pathlib
import re
from skimage.io import imread

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

Expand DownExpand Up@@ -205,7 +206,6 @@ def parse_phase() -> Phase:
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }

 )
 self.loaded_data.add(
 'band_slope', data['BS'].reshape(shape),
Expand DownExpand Up@@ -791,13 +791,31 @@ def load(self, file_name: pathlib.Path) -> None:
 self.check_data()


def load_image(file_name: pathlib.Path) -> Datastore:
 image = imread(file_name, as_gray=True)
 loaded_metadata = {
 'shape': image.shape,
 }
 laoded_data = Datastore()
 laoded_data.add(
 'image', image, unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': False,
 'cmap': 'gray',
 }
 )
 return loaded_metadata, laoded_data


def read_until_string(
 file: TextIO,
 term_string: str,
 comment_char: str = '*',
 line_process: Optional[Callable[[str], Any]] = None,
 exact: bool = False
) -> List[Any]:


 """Read lines in a file until a line starting with the `termString`
 is encountered. The file position is returned before the line starting
 with the `termString` when found. Comment and empty lines are ignored.
Expand Down

2 changes: 1 addition & 1 deletion
defdap/file_writers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
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('^' + ".*" + '
Adding a class for images by rhysgt · Pull Request #133 · MechMicroMan/DefDAP · GitHub
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Adding a class for images#133

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Adding a class for images
#133
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97ab620

Added optical class with import functions

Sep 29, 2024
b5452d4

Worked until add_homog_points

Oct 2, 2024
a1bce2b

Updates to optical image class


mikesmic Oct 15, 2024
3979d33

Initial commit

Nov 13, 2024
3970507

alltrue depreceated


rhysgt Nov 20, 2024
1bd2a4f

Fix unit cell plotting


rhysgt Nov 21, 2024
cb1ffd2

Combine optical and hrdic grain inspectors


rhysgt Nov 21, 2024
0794327

Update copyright year


rhysgt Nov 21, 2024
15f873b

Remove reference to DIC


rhysgt Nov 21, 2024
6b33a60

Tidy example optical notebook


rhysgt Nov 21, 2024
b6cfe6d

Update optical.ipynb


rhysgt Nov 21, 2024
3f4c4d1

Implement mixin class for hrdic/optical


rhysgt Dec 8, 2024
16ee030

Generalise rotate_data for 90, 180, 270 degree rotations


rhysgt Dec 8, 2024

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3 changes: 2 additions & 1 deletion
defdap/base.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -921,6 +921,7 @@ def grain_data(self, map_data):

 return grain_data


 def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
 """Extract a single grain map from the given map data.

Expand Down

2 changes: 1 addition & 1 deletion
defdap/crystal.py

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down

41 changes: 27 additions & 14 deletions
defdap/ebsd.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -242,21 +242,34 @@ def scale(self):
 return self.step_size

 @report_progress("rotating EBSD data")
 def rotate_data(self):
 """Rotate map by 180 degrees and transform quats accordingly.
 def rotate_data(self, angle=180):
 """Rotate map counter-clockwise by the specified angle (90, 180, 270 degrees) 
 and transform quats accordingly.

 """

 self.data.euler_angle = self.data.euler_angle[:, ::-1, ::-1]
 self.data.band_contrast = self.data.band_contrast[::-1, ::-1]
 self.data.band_slope = self.data.band_slope[::-1, ::-1]
 self.data.phase = self.data.phase[::-1, ::-1]
 self.calc_quat_array()

 # Rotation from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.pi).conjugate
 Parameters
 ----------
 angle : int
 The angle to rotate the map. Must be one of [90, 180, 270].

 # Perform vectorised multiplication
 """
 if angle not in [90, 180, 270]:
 raise ValueError("Angle must be one of [90, 180, 270]")

 # Rotate the data arrays by the specified angle
 k = angle // 90 # Number of 90 degree rotations

 # Change the shape of the EBSD data to match
 if k % 2 == 1:
 self.shape = self.shape[::-1]

 self.data.euler_angle = np.rot90(self.data.euler_angle, k=k, axes=(1, 2))
 self.data.band_contrast = np.rot90(self.data.band_contrast, k=k)
 self.data.mean_angular_deviation = np.rot90(self.data.mean_angular_deviation, k=k)
 self.data.band_slope = np.rot90(self.data.band_slope, k=k)
 self.data.phase = np.rot90(self.data.phase, k=k)

 # Rotation quaterions from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.deg2rad(-angle)).conjugate
 quats = Quat.multiply_many_quats(self.data.orientation.flatten(), transform_quat)
 self.data.orientation = np.array(quats).reshape(self.shape)

Expand Down

22 changes: 20 additions & 2 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand All@@ -19,6 +19,7 @@
from abc import ABC, abstractmethod
import pathlib
import re
from skimage.io import imread

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

Expand DownExpand Up@@ -205,7 +206,6 @@ def parse_phase() -> Phase:
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }

 )
 self.loaded_data.add(
 'band_slope', data['BS'].reshape(shape),
Expand DownExpand Up@@ -791,13 +791,31 @@ def load(self, file_name: pathlib.Path) -> None:
 self.check_data()


def load_image(file_name: pathlib.Path) -> Datastore:
 image = imread(file_name, as_gray=True)
 loaded_metadata = {
 'shape': image.shape,
 }
 laoded_data = Datastore()
 laoded_data.add(
 'image', image, unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': False,
 'cmap': 'gray',
 }
 )
 return loaded_metadata, laoded_data


def read_until_string(
 file: TextIO,
 term_string: str,
 comment_char: str = '*',
 line_process: Optional[Callable[[str], Any]] = None,
 exact: bool = False
) -> List[Any]:


 """Read lines in a file until a line starting with the `termString`
 is encountered. The file position is returned before the line starting
 with the `termString` when found. Comment and empty lines are ignored.
Expand Down

2 changes: 1 addition & 1 deletion
defdap/file_writers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
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" + '
Adding a class for images by rhysgt · Pull Request #133 · MechMicroMan/DefDAP · GitHub
Skip to content
Adding a class for images#133

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 Open

rhysgt
wants to merge
13
commits into

base:develop
Choose a base branch

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Adding a class for images
#133
Show file tree
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13 commits


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Hold shift + click to select a range
97ab620

Added optical class with import functions

Sep 29, 2024
b5452d4

Worked until add_homog_points

Oct 2, 2024
a1bce2b

Updates to optical image class


mikesmic Oct 15, 2024
3979d33

Initial commit

Nov 13, 2024
3970507

alltrue depreceated


rhysgt Nov 20, 2024
1bd2a4f

Fix unit cell plotting


rhysgt Nov 21, 2024
cb1ffd2

Combine optical and hrdic grain inspectors


rhysgt Nov 21, 2024
0794327

Update copyright year


rhysgt Nov 21, 2024
15f873b

Remove reference to DIC


rhysgt Nov 21, 2024
6b33a60

Tidy example optical notebook


rhysgt Nov 21, 2024
b6cfe6d

Update optical.ipynb


rhysgt Nov 21, 2024
3f4c4d1

Implement mixin class for hrdic/optical


rhysgt Dec 8, 2024
16ee030

Generalise rotate_data for 90, 180, 270 degree rotations


rhysgt Dec 8, 2024

File filter

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3 changes: 2 additions & 1 deletion
defdap/base.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -921,6 +921,7 @@ def grain_data(self, map_data):

 return grain_data


 def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
 """Extract a single grain map from the given map data.

Expand Down

2 changes: 1 addition & 1 deletion
defdap/crystal.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down

41 changes: 27 additions & 14 deletions
defdap/ebsd.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -242,21 +242,34 @@ def scale(self):
 return self.step_size

 @report_progress("rotating EBSD data")
 def rotate_data(self):
 """Rotate map by 180 degrees and transform quats accordingly.
 def rotate_data(self, angle=180):
 """Rotate map counter-clockwise by the specified angle (90, 180, 270 degrees) 
 and transform quats accordingly.

 """

 self.data.euler_angle = self.data.euler_angle[:, ::-1, ::-1]
 self.data.band_contrast = self.data.band_contrast[::-1, ::-1]
 self.data.band_slope = self.data.band_slope[::-1, ::-1]
 self.data.phase = self.data.phase[::-1, ::-1]
 self.calc_quat_array()

 # Rotation from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.pi).conjugate
 Parameters
 ----------
 angle : int
 The angle to rotate the map. Must be one of [90, 180, 270].

 # Perform vectorised multiplication
 """
 if angle not in [90, 180, 270]:
 raise ValueError("Angle must be one of [90, 180, 270]")

 # Rotate the data arrays by the specified angle
 k = angle // 90 # Number of 90 degree rotations

 # Change the shape of the EBSD data to match
 if k % 2 == 1:
 self.shape = self.shape[::-1]

 self.data.euler_angle = np.rot90(self.data.euler_angle, k=k, axes=(1, 2))
 self.data.band_contrast = np.rot90(self.data.band_contrast, k=k)
 self.data.mean_angular_deviation = np.rot90(self.data.mean_angular_deviation, k=k)
 self.data.band_slope = np.rot90(self.data.band_slope, k=k)
 self.data.phase = np.rot90(self.data.phase, k=k)

 # Rotation quaterions from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.deg2rad(-angle)).conjugate
 quats = Quat.multiply_many_quats(self.data.orientation.flatten(), transform_quat)
 self.data.orientation = np.array(quats).reshape(self.shape)

Expand Down

22 changes: 20 additions & 2 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand All@@ -19,6 +19,7 @@
from abc import ABC, abstractmethod
import pathlib
import re
from skimage.io import imread

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

Expand DownExpand Up@@ -205,7 +206,6 @@ def parse_phase() -> Phase:
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }

 )
 self.loaded_data.add(
 'band_slope', data['BS'].reshape(shape),
Expand DownExpand Up@@ -791,13 +791,31 @@ def load(self, file_name: pathlib.Path) -> None:
 self.check_data()


def load_image(file_name: pathlib.Path) -> Datastore:
 image = imread(file_name, as_gray=True)
 loaded_metadata = {
 'shape': image.shape,
 }
 laoded_data = Datastore()
 laoded_data.add(
 'image', image, unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': False,
 'cmap': 'gray',
 }
 )
 return loaded_metadata, laoded_data


def read_until_string(
 file: TextIO,
 term_string: str,
 comment_char: str = '*',
 line_process: Optional[Callable[[str], Any]] = None,
 exact: bool = False
) -> List[Any]:


 """Read lines in a file until a line starting with the `termString`
 is encountered. The file position is returned before the line starting
 with the `termString` when found. Comment and empty lines are ignored.
Expand Down

2 changes: 1 addition & 1 deletion
defdap/file_writers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
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('^' + ".*" + '
Adding a class for images by rhysgt · Pull Request #133 · MechMicroMan/DefDAP · GitHub
Skip to content
Adding a class for images#133

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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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to your account

 Open

rhysgt
wants to merge
13
commits into

base:develop
Choose a base branch

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Adding a class for images
#133
Show file tree
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13 commits


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Hold shift + click to select a range
97ab620

Added optical class with import functions

Sep 29, 2024
b5452d4

Worked until add_homog_points

Oct 2, 2024
a1bce2b

Updates to optical image class


mikesmic Oct 15, 2024
3979d33

Initial commit

Nov 13, 2024
3970507

alltrue depreceated


rhysgt Nov 20, 2024
1bd2a4f

Fix unit cell plotting


rhysgt Nov 21, 2024
cb1ffd2

Combine optical and hrdic grain inspectors


rhysgt Nov 21, 2024
0794327

Update copyright year


rhysgt Nov 21, 2024
15f873b

Remove reference to DIC


rhysgt Nov 21, 2024
6b33a60

Tidy example optical notebook


rhysgt Nov 21, 2024
b6cfe6d

Update optical.ipynb


rhysgt Nov 21, 2024
3f4c4d1

Implement mixin class for hrdic/optical


rhysgt Dec 8, 2024
16ee030

Generalise rotate_data for 90, 180, 270 degree rotations


rhysgt Dec 8, 2024

File filter

Filter by extension
Filter by extension
Conversations

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Loading
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3 changes: 2 additions & 1 deletion
defdap/base.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -921,6 +921,7 @@ def grain_data(self, map_data):

 return grain_data


 def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
 """Extract a single grain map from the given map data.

Expand Down

2 changes: 1 addition & 1 deletion
defdap/crystal.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down

41 changes: 27 additions & 14 deletions
defdap/ebsd.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -242,21 +242,34 @@ def scale(self):
 return self.step_size

 @report_progress("rotating EBSD data")
 def rotate_data(self):
 """Rotate map by 180 degrees and transform quats accordingly.
 def rotate_data(self, angle=180):
 """Rotate map counter-clockwise by the specified angle (90, 180, 270 degrees) 
 and transform quats accordingly.

 """

 self.data.euler_angle = self.data.euler_angle[:, ::-1, ::-1]
 self.data.band_contrast = self.data.band_contrast[::-1, ::-1]
 self.data.band_slope = self.data.band_slope[::-1, ::-1]
 self.data.phase = self.data.phase[::-1, ::-1]
 self.calc_quat_array()

 # Rotation from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.pi).conjugate
 Parameters
 ----------
 angle : int
 The angle to rotate the map. Must be one of [90, 180, 270].

 # Perform vectorised multiplication
 """
 if angle not in [90, 180, 270]:
 raise ValueError("Angle must be one of [90, 180, 270]")

 # Rotate the data arrays by the specified angle
 k = angle // 90 # Number of 90 degree rotations

 # Change the shape of the EBSD data to match
 if k % 2 == 1:
 self.shape = self.shape[::-1]

 self.data.euler_angle = np.rot90(self.data.euler_angle, k=k, axes=(1, 2))
 self.data.band_contrast = np.rot90(self.data.band_contrast, k=k)
 self.data.mean_angular_deviation = np.rot90(self.data.mean_angular_deviation, k=k)
 self.data.band_slope = np.rot90(self.data.band_slope, k=k)
 self.data.phase = np.rot90(self.data.phase, k=k)

 # Rotation quaterions from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.deg2rad(-angle)).conjugate
 quats = Quat.multiply_many_quats(self.data.orientation.flatten(), transform_quat)
 self.data.orientation = np.array(quats).reshape(self.shape)

Expand Down

22 changes: 20 additions & 2 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand All@@ -19,6 +19,7 @@
from abc import ABC, abstractmethod
import pathlib
import re
from skimage.io import imread

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

Expand DownExpand Up@@ -205,7 +206,6 @@ def parse_phase() -> Phase:
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }

 )
 self.loaded_data.add(
 'band_slope', data['BS'].reshape(shape),
Expand DownExpand Up@@ -791,13 +791,31 @@ def load(self, file_name: pathlib.Path) -> None:
 self.check_data()


def load_image(file_name: pathlib.Path) -> Datastore:
 image = imread(file_name, as_gray=True)
 loaded_metadata = {
 'shape': image.shape,
 }
 laoded_data = Datastore()
 laoded_data.add(
 'image', image, unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': False,
 'cmap': 'gray',
 }
 )
 return loaded_metadata, laoded_data


def read_until_string(
 file: TextIO,
 term_string: str,
 comment_char: str = '*',
 line_process: Optional[Callable[[str], Any]] = None,
 exact: bool = False
) -> List[Any]:


 """Read lines in a file until a line starting with the `termString`
 is encountered. The file position is returned before the line starting
 with the `termString` when found. Comment and empty lines are ignored.
Expand Down

2 changes: 1 addition & 1 deletion
defdap/file_writers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Adding a class for images by rhysgt · Pull Request #133 · MechMicroMan/DefDAP · GitHub
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Adding a class for images#133

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Adding a class for images
#133
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97ab620

Added optical class with import functions

Sep 29, 2024
b5452d4

Worked until add_homog_points

Oct 2, 2024
a1bce2b

Updates to optical image class


mikesmic Oct 15, 2024
3979d33

Initial commit

Nov 13, 2024
3970507

alltrue depreceated


rhysgt Nov 20, 2024
1bd2a4f

Fix unit cell plotting


rhysgt Nov 21, 2024
cb1ffd2

Combine optical and hrdic grain inspectors


rhysgt Nov 21, 2024
0794327

Update copyright year


rhysgt Nov 21, 2024
15f873b

Remove reference to DIC


rhysgt Nov 21, 2024
6b33a60

Tidy example optical notebook


rhysgt Nov 21, 2024
b6cfe6d

Update optical.ipynb


rhysgt Nov 21, 2024
3f4c4d1

Implement mixin class for hrdic/optical


rhysgt Dec 8, 2024
16ee030

Generalise rotate_data for 90, 180, 270 degree rotations


rhysgt Dec 8, 2024

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3 changes: 2 additions & 1 deletion
defdap/base.py

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -921,6 +921,7 @@ def grain_data(self, map_data):

 return grain_data


 def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
 """Extract a single grain map from the given map data.

Expand Down

2 changes: 1 addition & 1 deletion
defdap/crystal.py

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down

41 changes: 27 additions & 14 deletions
defdap/ebsd.py

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -242,21 +242,34 @@ def scale(self):
 return self.step_size

 @report_progress("rotating EBSD data")
 def rotate_data(self):
 """Rotate map by 180 degrees and transform quats accordingly.
 def rotate_data(self, angle=180):
 """Rotate map counter-clockwise by the specified angle (90, 180, 270 degrees) 
 and transform quats accordingly.

 """

 self.data.euler_angle = self.data.euler_angle[:, ::-1, ::-1]
 self.data.band_contrast = self.data.band_contrast[::-1, ::-1]
 self.data.band_slope = self.data.band_slope[::-1, ::-1]
 self.data.phase = self.data.phase[::-1, ::-1]
 self.calc_quat_array()

 # Rotation from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.pi).conjugate
 Parameters
 ----------
 angle : int
 The angle to rotate the map. Must be one of [90, 180, 270].

 # Perform vectorised multiplication
 """
 if angle not in [90, 180, 270]:
 raise ValueError("Angle must be one of [90, 180, 270]")

 # Rotate the data arrays by the specified angle
 k = angle // 90 # Number of 90 degree rotations

 # Change the shape of the EBSD data to match
 if k % 2 == 1:
 self.shape = self.shape[::-1]

 self.data.euler_angle = np.rot90(self.data.euler_angle, k=k, axes=(1, 2))
 self.data.band_contrast = np.rot90(self.data.band_contrast, k=k)
 self.data.mean_angular_deviation = np.rot90(self.data.mean_angular_deviation, k=k)
 self.data.band_slope = np.rot90(self.data.band_slope, k=k)
 self.data.phase = np.rot90(self.data.phase, k=k)

 # Rotation quaterions from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.deg2rad(-angle)).conjugate
 quats = Quat.multiply_many_quats(self.data.orientation.flatten(), transform_quat)
 self.data.orientation = np.array(quats).reshape(self.shape)

Expand Down

22 changes: 20 additions & 2 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand All@@ -19,6 +19,7 @@
from abc import ABC, abstractmethod
import pathlib
import re
from skimage.io import imread

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

Expand DownExpand Up@@ -205,7 +206,6 @@ def parse_phase() -> Phase:
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }

 )
 self.loaded_data.add(
 'band_slope', data['BS'].reshape(shape),
Expand DownExpand Up@@ -791,13 +791,31 @@ def load(self, file_name: pathlib.Path) -> None:
 self.check_data()


def load_image(file_name: pathlib.Path) -> Datastore:
 image = imread(file_name, as_gray=True)
 loaded_metadata = {
 'shape': image.shape,
 }
 laoded_data = Datastore()
 laoded_data.add(
 'image', image, unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': False,
 'cmap': 'gray',
 }
 )
 return loaded_metadata, laoded_data


def read_until_string(
 file: TextIO,
 term_string: str,
 comment_char: str = '*',
 line_process: Optional[Callable[[str], Any]] = None,
 exact: bool = False
) -> List[Any]:


 """Read lines in a file until a line starting with the `termString`
 is encountered. The file position is returned before the line starting
 with the `termString` when found. Comment and empty lines are ignored.
Expand Down

2 changes: 1 addition & 1 deletion
defdap/file_writers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
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); }
})();
})();
Adding a class for images by rhysgt · Pull Request #133 · MechMicroMan/DefDAP · GitHub
Skip to content
Adding a class for images#133

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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
to your account

 Open

rhysgt
wants to merge
13
commits into

base:develop
Choose a base branch

from

 Open


Adding a class for images
#133
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


13 commits


Select commit
Hold shift + click to select a range
97ab620

Added optical class with import functions

Sep 29, 2024
b5452d4

Worked until add_homog_points

Oct 2, 2024
a1bce2b

Updates to optical image class


mikesmic Oct 15, 2024
3979d33

Initial commit

Nov 13, 2024
3970507

alltrue depreceated


rhysgt Nov 20, 2024
1bd2a4f

Fix unit cell plotting


rhysgt Nov 21, 2024
cb1ffd2

Combine optical and hrdic grain inspectors


rhysgt Nov 21, 2024
0794327

Update copyright year


rhysgt Nov 21, 2024
15f873b

Remove reference to DIC


rhysgt Nov 21, 2024
6b33a60

Tidy example optical notebook


rhysgt Nov 21, 2024
b6cfe6d

Update optical.ipynb


rhysgt Nov 21, 2024
3f4c4d1

Implement mixin class for hrdic/optical


rhysgt Dec 8, 2024
16ee030

Generalise rotate_data for 90, 180, 270 degree rotations


rhysgt Dec 8, 2024

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

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Failed to load files. 
Loading
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3 changes: 2 additions & 1 deletion
defdap/base.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -921,6 +921,7 @@ def grain_data(self, map_data):

 return grain_data


 def grain_map_data(self, map_data=None, grain_data=None, bg=np.nan):
 """Extract a single grain map from the given map data.

Expand Down

2 changes: 1 addition & 1 deletion
defdap/crystal.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down

41 changes: 27 additions & 14 deletions
defdap/ebsd.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand DownExpand Up@@ -242,21 +242,34 @@ def scale(self):
 return self.step_size

 @report_progress("rotating EBSD data")
 def rotate_data(self):
 """Rotate map by 180 degrees and transform quats accordingly.
 def rotate_data(self, angle=180):
 """Rotate map counter-clockwise by the specified angle (90, 180, 270 degrees) 
 and transform quats accordingly.

 """

 self.data.euler_angle = self.data.euler_angle[:, ::-1, ::-1]
 self.data.band_contrast = self.data.band_contrast[::-1, ::-1]
 self.data.band_slope = self.data.band_slope[::-1, ::-1]
 self.data.phase = self.data.phase[::-1, ::-1]
 self.calc_quat_array()

 # Rotation from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.pi).conjugate
 Parameters
 ----------
 angle : int
 The angle to rotate the map. Must be one of [90, 180, 270].

 # Perform vectorised multiplication
 """
 if angle not in [90, 180, 270]:
 raise ValueError("Angle must be one of [90, 180, 270]")

 # Rotate the data arrays by the specified angle
 k = angle // 90 # Number of 90 degree rotations

 # Change the shape of the EBSD data to match
 if k % 2 == 1:
 self.shape = self.shape[::-1]

 self.data.euler_angle = np.rot90(self.data.euler_angle, k=k, axes=(1, 2))
 self.data.band_contrast = np.rot90(self.data.band_contrast, k=k)
 self.data.mean_angular_deviation = np.rot90(self.data.mean_angular_deviation, k=k)
 self.data.band_slope = np.rot90(self.data.band_slope, k=k)
 self.data.phase = np.rot90(self.data.phase, k=k)

 # Rotation quaterions from old coord system to new
 transform_quat = Quat.from_axis_angle(np.array([0, 0, 1]), np.deg2rad(-angle)).conjugate
 quats = Quat.multiply_many_quats(self.data.orientation.flatten(), transform_quat)
 self.data.orientation = np.array(quats).reshape(self.shape)

Expand Down

22 changes: 20 additions & 2 deletions
defdap/file_readers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand All@@ -19,6 +19,7 @@
from abc import ABC, abstractmethod
import pathlib
import re
from skimage.io import imread

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

Expand DownExpand Up@@ -205,7 +206,6 @@ def parse_phase() -> Phase:
 'cmap': 'gray',
 'clabel': 'Band contrast',
 }

 )
 self.loaded_data.add(
 'band_slope', data['BS'].reshape(shape),
Expand DownExpand Up@@ -791,13 +791,31 @@ def load(self, file_name: pathlib.Path) -> None:
 self.check_data()


def load_image(file_name: pathlib.Path) -> Datastore:
 image = imread(file_name, as_gray=True)
 loaded_metadata = {
 'shape': image.shape,
 }
 laoded_data = Datastore()
 laoded_data.add(
 'image', image, unit='', type='map', order=0,
 plot_params={
 'plot_colour_bar': False,
 'cmap': 'gray',
 }
 )
 return loaded_metadata, laoded_data


def read_until_string(
 file: TextIO,
 term_string: str,
 comment_char: str = '*',
 line_process: Optional[Callable[[str], Any]] = None,
 exact: bool = False
) -> List[Any]:


 """Read lines in a file until a line starting with the `termString`
 is encountered. The file position is returned before the line starting
 with the `termString` when found. Comment and empty lines are ignored.
Expand Down

2 changes: 1 addition & 1 deletion
defdap/file_writers.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
# Copyright 2023 Mechanics of Microstructures Group
# Copyright 2024 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
Expand Down
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