diff --git a/README.md b/README.md index 44ff407..ed4678f 100755 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@

-![version](https://img.shields.io/badge/package_version-0.1.3-orange) +![version](https://img.shields.io/badge/package_version-0.1.4-orange) ![PyPI status](https://img.shields.io/pypi/status/ansicolortags.svg) ![license](https://img.shields.io/github/license/mashape/apistatus.svg) ![Open Source Love](https://img.shields.io/badge/open%20source-♡-lightgrey) diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo index 731aa3f..5ec3de6 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 8d3dece494f9aa6c3ab1b26769a86beb +config: 02015b5d8e133bda0ea82d8b84874b12 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_images/d8fe0e40ef759b57b7816b7bdaa94c7f165a8e2c217e274c8b33931b7b9669ab.png b/docs/_build/html/_images/d8fe0e40ef759b57b7816b7bdaa94c7f165a8e2c217e274c8b33931b7b9669ab.png new file mode 100644 index 0000000..111b966 Binary files /dev/null and b/docs/_build/html/_images/d8fe0e40ef759b57b7816b7bdaa94c7f165a8e2c217e274c8b33931b7b9669ab.png differ diff --git a/docs/_build/html/_sources/_autosummary/pykanto.utils.types.rst.txt b/docs/_build/html/_sources/_autosummary/pykanto.utils.types.rst.txt index 33e095b..f85c7f1 100644 --- a/docs/_build/html/_sources/_autosummary/pykanto.utils.types.rst.txt +++ b/docs/_build/html/_sources/_autosummary/pykanto.utils.types.rst.txt @@ -1,4 +1,4 @@ -pykanto.utils.types +pykanto.utils.types =================== .. automodule:: pykanto.utils.types diff --git a/docs/_build/html/_sources/index.md.txt b/docs/_build/html/_sources/index.md.txt index be9a0f7..7d5c047 100644 --- a/docs/_build/html/_sources/index.md.txt +++ b/docs/_build/html/_sources/index.md.txt @@ -9,7 +9,7 @@ more reproducible. This website contains its documentation.
it to analyse bird songs. ![Python 3.8](https://img.shields.io/badge/_python-≥3.8-lighgreen.svg) -![version](https://img.shields.io/badge/_version-0.1.0-orange.svg) +![version](https://img.shields.io/badge/_version-0.1.4-orange.svg)
diff --git a/docs/_build/html/_static/copybutton.css b/docs/_build/html/_static/copybutton.css index f1916ec..40eafe5 100644 --- a/docs/_build/html/_static/copybutton.css +++ b/docs/_build/html/_static/copybutton.css @@ -35,8 +35,7 @@ div.highlight { position: relative; } -/* Show the copybutton */ -.highlight:hover button.copybtn, button.copybtn.success { +.highlight:hover button.copybtn { opacity: 1; } diff --git a/docs/_build/html/_static/copybutton.js b/docs/_build/html/_static/copybutton.js index 751cbb4..307a14f 100644 --- a/docs/_build/html/_static/copybutton.js +++ b/docs/_build/html/_static/copybutton.js @@ -102,25 +102,18 @@ const clearSelection = () => { } } -// Changes tooltip text for a moment, then changes it back -// We want the timeout of our `success` class to be a bit shorter than the -// tooltip and icon change, so that we can hide the icon before changing back. -var timeoutIcon = 2000; -var timeoutSuccessClass = 1500; - +// Changes tooltip text for two seconds, then changes it back const temporarilyChangeTooltip = (el, oldText, newText) => { el.setAttribute('data-tooltip', newText) el.classList.add('success') - // Remove success a little bit sooner than we change the tooltip - // So that we can use CSS to hide the copybutton first - setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) - setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) + setTimeout(() => el.setAttribute('data-tooltip', oldText), 2000) + setTimeout(() => el.classList.remove('success'), 2000) } // Changes the copy button icon for two seconds, then changes it back const temporarilyChangeIcon = (el) => { el.innerHTML = iconCheck; - setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) + setTimeout(() => {el.innerHTML = iconCopy}, 2000) } const addCopyButtonToCodeCells = () => { @@ -132,8 +125,7 @@ const addCopyButtonToCodeCells = () => { } // Add copybuttons to all of our code cells - const COPYBUTTON_SELECTOR = 'div.highlight pre'; - const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) + const codeCells = document.querySelectorAll('div.highlight pre') codeCells.forEach((codeCell, index) => { const id = codeCellId(index) codeCell.setAttribute('id', id) @@ -149,25 +141,10 @@ function escapeRegExp(string) { return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string } -/** - * Removes excluded text from a Node. - * - * @param {Node} target Node to filter. - * @param {string} exclude CSS selector of nodes to exclude. - * @returns {DOMString} Text from `target` with text removed. - */ -function filterText(target, exclude) { - const clone = target.cloneNode(true); // clone as to not modify the live DOM - if (exclude) { - // remove excluded nodes - clone.querySelectorAll(exclude).forEach(node => node.remove()); - } - return clone.innerText; -} - // Callback when a copy button is clicked. Will be passed the node that was clicked // should then grab the text and replace pieces of text that shouldn't be used in output function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; var match; @@ -222,12 +199,7 @@ function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onl var copyTargetText = (trigger) => { var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); - - // get filtered text - let exclude = '.linenos, .gp'; - - let text = filterText(target, exclude); - return formatCopyText(text, '>>> |^\\d+|\\.\\.\\. |\\$ |In \\[\\d*\\]: | {2,5}\\.\\.\\.: | {5,8}: ', true, true, true, true, '', '') + return formatCopyText(target.innerText, '>>> |^\\d+|\\.\\.\\. |\\$ |In \\[\\d*\\]: | {2,5}\\.\\.\\.: | {5,8}: ', true, true, true, true, '', '') } // Initialize with a callback so we can modify the text before copy diff --git a/docs/_build/html/_static/copybutton_funcs.js b/docs/_build/html/_static/copybutton_funcs.js index dbe1aaa..b9168c5 100644 --- a/docs/_build/html/_static/copybutton_funcs.js +++ b/docs/_build/html/_static/copybutton_funcs.js @@ -2,25 +2,10 @@ function escapeRegExp(string) { return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string } -/** - * Removes excluded text from a Node. - * - * @param {Node} target Node to filter. - * @param {string} exclude CSS selector of nodes to exclude. - * @returns {DOMString} Text from `target` with text removed. - */ -export function filterText(target, exclude) { - const clone = target.cloneNode(true); // clone as to not modify the live DOM - if (exclude) { - // remove excluded nodes - clone.querySelectorAll(exclude).forEach(node => node.remove()); - } - return clone.innerText; -} - // Callback when a copy button is clicked. Will be passed the node that was clicked // should then grab the text and replace pieces of text that shouldn't be used in output export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { + var regexp; var match; diff --git a/docs/_build/html/_static/pygments.css b/docs/_build/html/_static/pygments.css index f227e5c..c5d3a66 100644 --- a/docs/_build/html/_static/pygments.css +++ b/docs/_build/html/_static/pygments.css @@ -54,7 +54,6 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: .highlight .nt { color: #204a87; font-weight: bold } /* Name.Tag */ .highlight .nv { color: #000000 } /* Name.Variable */ .highlight .ow { color: #204a87; font-weight: bold } /* Operator.Word */ -.highlight .pm { color: #000000; font-weight: bold } /* Punctuation.Marker */ .highlight .w { color: #f8f8f8 } /* Text.Whitespace */ .highlight .mb { color: #0000cf; font-weight: bold } /* Literal.Number.Bin */ .highlight .mf { color: #0000cf; font-weight: bold } /* Literal.Number.Float */ diff --git a/docs/_build/html/contents/basic-workflow.html b/docs/_build/html/contents/basic-workflow.html index d54e8e7..e5abc24 100644 --- a/docs/_build/html/contents/basic-workflow.html +++ b/docs/_build/html/contents/basic-workflow.html @@ -36,7 +36,7 @@ - + @@ -522,10 +522,10 @@

Basic workflowHide code cell outputs
-
2023-02-28 11:36:45,976	INFO worker.py:1519 -- Started a local Ray instance. View the dashboard at 127.0.0.1:8266 
+
2023-03-14 22:06:28,462	INFO services.py:1456 -- View the Ray dashboard at http://127.0.0.1:8265
 

 

-
Done
+
Done
 

 

 

@@ -556,17 +556,15 @@ 
Basic workflow
-
Using existing unit onset/offset information.
-Found and segmented 169 units.
+
Found and segmented 169 units.
 

 

-
UserWarning:
-    The vocalisations in this dataset have already been segmented: will use existing segmentation information.If you want to do it again, you can overwrite the existing segmentation information by it by setting `overwrite=True`
-

-

-../_images/091fffa1c923b9ed27c40dfc1cf0569debba2f9b1e6320f66ae4e65a99f3845e.png
+../_images/d8fe0e40ef759b57b7816b7bdaa94c7f165a8e2c217e274c8b33931b7b9669ab.png
 

 

 
Next, you can create spectrogram representations of the units or the average of the units present in the vocalisations of each individual ID in the dataset, project and cluster them, and prepare compressed representations that can be used with the interactive app:

@@ -696,19 +682,19 @@ 
Basic workflowHide code cell outputs
 
 

-
Found 2 individual IDs. They will be processed in 2 chunks of length 1.
+
Found 2 individual IDs. They will be processed in 2 chunks of length 1.
 

 

-
Found 2 individual IDs. They will be processed in 2 chunks of length 1.
+
Found 2 individual IDs. They will be processed in 2 chunks of length 1.
 

 

-
(_reduce_and_cluster_r pid=138856) UserWarning:
-(_reduce_and_cluster_r pid=138856)     `min_cluster_size` too small, setting it to 2
-(_reduce_and_cluster_r pid=138855) UserWarning:
-(_reduce_and_cluster_r pid=138855)     `min_cluster_size` too small, setting it to 2
+
(_reduce_and_cluster_r pid=71705) UserWarning:
+(_reduce_and_cluster_r pid=71705)     `min_cluster_size` too small, setting it to 2
+(_reduce_and_cluster_r pid=71708) UserWarning:
+(_reduce_and_cluster_r pid=71708)     `min_cluster_size` too small, setting it to 2
 

 

-

+

 
 

 
Now you can start the interactive app on your browser by simply running dataset.open_label_app().

diff --git a/docs/_build/html/contents/feature-extraction.html b/docs/_build/html/contents/feature-extraction.html
index 4a0b2ec..fe674bf 100644
--- a/docs/_build/html/contents/feature-extraction.html
+++ b/docs/_build/html/contents/feature-extraction.html
@@ -36,7 +36,7 @@
     
     
     
-    
+    
     
     
     
@@ -601,16 +601,16 @@ 
Acoustic feature extraction
Found 2 files. They will be processed in 2 chunks of length 1.
 

 

-
2023-02-28 11:37:14,369	INFO worker.py:1519 -- Started a local Ray instance. View the dashboard at 127.0.0.1:8266 
+
2023-02-20 21:20:12,234	INFO worker.py:1529 -- Started a local Ray instance. View the dashboard at 127.0.0.1:8265 
 

 

-
Function 'segment_files_parallel' took 4.5977 sec.
+
Function 'segment_files_parallel' took 6.5322 sec.
 

 

-
Function 'chipper_units_to_json' took 0.8491 sec.
+
Function 'chipper_units_to_json' took 0.9984 sec.
 

 

-
Done
+
Done
 Using existing unit onset/offset information.
 Found and segmented 527 units.
 

@@ -641,7 +641,7 @@ 
Acoustic feature extraction
-../_images/82eda62704d0e7111bb471d7e471a751c8b80bfa8945f2d37662b172ca34da46.png
+../_images/d22eb0d699fee0dd88f2afcb173c292131ca47fcc15adace69426a60fce1d29f.png
 

 

 
Now that the data are ready, we can extract some features from the spectrograms.
diff --git a/docs/_build/html/contents/kantodata-dataset.html b/docs/_build/html/contents/kantodata-dataset.html
index 35ac026..289618e 100644
--- a/docs/_build/html/contents/kantodata-dataset.html
+++ b/docs/_build/html/contents/kantodata-dataset.html
@@ -36,7 +36,7 @@
     
     
     
-    
+    
     
     
     
diff --git a/docs/_build/html/contents/segmenting-files.html b/docs/_build/html/contents/segmenting-files.html
index 062f2bb..09901f2 100644
--- a/docs/_build/html/contents/segmenting-files.html
+++ b/docs/_build/html/contents/segmenting-files.html
@@ -36,7 +36,7 @@
     
     
     
-    
+    
     
     
     
diff --git a/docs/_build/html/contents/segmenting-vocalisations.html b/docs/_build/html/contents/segmenting-vocalisations.html
index eb3c93a..968cf51 100644
--- a/docs/_build/html/contents/segmenting-vocalisations.html
+++ b/docs/_build/html/contents/segmenting-vocalisations.html
@@ -36,7 +36,7 @@
     
     
     
-    
+    
     
     
     
@@ -593,10 +593,10 @@ 
Segmenting vocalisations into unitsHide code cell outputs
 
 

-
2023-02-28 11:38:21,187	INFO worker.py:1519 -- Started a local Ray instance. View the dashboard at 127.0.0.1:8266 
+
2023-02-20 21:21:55,947	INFO worker.py:1529 -- Started a local Ray instance. View the dashboard at 127.0.0.1:8265 
 

 

-
Done
+
Done
 

 

 

@@ -613,7 +613,7 @@ 
Segmenting vocalisations into units
-../_images/0889f9f682e1d5f98ebc3344e87586e464c9494246fae7ee60ae668171184ec9.png
+../_images/5b46234493a475570de8ac0a5081aa1e6789b6a3f608e68177bf9498a214c160.png
 

 

 
Finally, to segment the vocalisations into units, we do the following:

@@ -624,7 +624,7 @@ 
Segmenting vocalisations into units
-
Found and segmented 268 units.
+
Found and segmented 268 units.
 

 

 

@@ -638,7 +638,7 @@ 
Segmenting vocalisations into units
-../_images/94979e30a3ffdf1a840e2740d3fd84deaf73a878f0775e68526ac571805ac139.png
+../_images/8c06259aaed31b63d3628f72a7a5f1d46b0d8a797feb889aad8778d147c51f91.png
 

 

 
If you want to access the onsets or offsets manually, simply get them from the dataset:

diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index 2929f17..d3c7681 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -487,7 +487,7 @@ 
Modules

 This article explains the motivation behind the project and provides a worked example using
 it to analyse bird songs.

 
Python 3.8
-version

+version

 

 

 
User guide

diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index 8a15585..b8f4ff9 100644
--- a/docs/_build/html/searchindex.js
+++ b/docs/_build/html/searchindex.js
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\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
index be9a0f7..7d5c047 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -9,7 +9,7 @@ more reproducible. This website contains its documentation.

 it to analyse bird songs.
 
 ![Python 3.8](https://img.shields.io/badge/_python-≥3.8-lighgreen.svg)
-![version](https://img.shields.io/badge/_version-0.1.0-orange.svg)
+![version](https://img.shields.io/badge/_version-0.1.4-orange.svg)