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Trevor Lancon tlancon

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tlancon / copy_lut_napari.py
Last active Jun 8, 2021
Copies the main visualization properties from one layer to another in napari.
View copy_lut_napari.py
def copy_lut(from_layer, to_layer, opacity=False):
"""
Copies the visualization properties from one layer to another in napari.
Only the colormap, contrast limits, and gamma values are included by default.
The opacity can be optionally copied as well.
Blending and interpolation are ignored.
@tlancon
tlancon / TrainWekaOnMultipleImages.ijm
Created Apr 2, 2021
Train a Weka model on multiple images by stacking slices from them together as a single stack. The stack is the same size in XY as the largest image, and all smaller images are padded with 0's to the lower-right corner to keep their original scale.
View TrainWekaOnMultipleImages.ijm
// Requirements:
// Trainable Weka Segmentation
// The list of files to use for training must be described in a text file,
// with each line containing the full path to one image.
listOfImages = File.openDialog("Choose a file with a list of images:");
imagesString = File.openAsString(listOfImages);
images = split(imagesString, "\n");
for (i=0; i<images.length; i++) {
@tlancon
tlancon / rip_gopro_audio.cmd
Last active Sep 29, 2020
Rips the audio from the all MP4s in the current directory to WAV. Requires FFMPEG.
View rip_gopro_audio.cmd
for /r %%f in (*MP4) do (
ffmpeg -i %%f -q:a 0 -map a "%%~nf.wav"
)
@tlancon
tlancon / reject_outliers.py
Created Jun 5, 2020
Reject outliers from a 1D signal based on a sliding window and a deviation threshold.
View reject_outliers.py
def reject_outliers(arr, window_size, threshold):
"""
Given a 1D signal, replace outliers with the average of the surrounding points.
Does the following for every point:
1. Computes the median of the sliding window
2. Computes the percentage difference between the current point and the
sliding window median
3. If that deviation exceeds the given threshold, replaces that point with
the average of the surrounding two points.
@tlancon
tlancon / InspectLine.py
Created May 28, 2020
Inspect labeled objects in an image touching either a horizontal or vertical center line. Information is printed to the console.
View InspectLine.py
import os
import numpy as np
import matplotlib.pyplot as plt
from skimage import io
from skimage.measure import regionprops
# ----------------------------------------------------------
# Input
wdir = os.path.dirname('<DIRECTORY_CONTAINING_IMAGES>')
fname = '<LABELED_IMAGE_NAME>.tif'
@tlancon
tlancon / distance_between_points.py
Created May 17, 2020
Calculate the distance between X, Y points saved arrays using NumPy's diff() function without a loop.
View distance_between_points.py
import numpy as np
x = np.array([0, 1, 2, 3, 4, 5])
y = np.array([4, 5, 6, 7, 8, 9])
displacement = np.sqrt(np.diff(x, prepend=x[0])**2 + np.diff(y, prepend=y[0])**2)
@tlancon
tlancon / napari_count_tfpn.py
Last active Mar 24, 2022
Call this function to launch a napari window with a given image to begin annotating true positives, false positives, and false negatives on the image with points layers.
View napari_count_tfpn.py
import os
import napari
from skimage.io import imread, imsave
def napari_count_tfpn(screenshot_file, point_size=20, save_screenshot=True):
"""
Opens a napari window and initializes three points layers:
- "True Positives" with green points
- "False Positives" with red points
- "False Negatives" with yellow points
@tlancon
tlancon / sarcastify.py
Last active Jul 2, 2019
Make any string sarcastic!
View sarcastify.py
def sarcastify(my_string):
"""
Returns a sarcastic version of the provided string.
Example:
>>> sarcastify('Do you really think that\'s a good idea?')
"dO YoU ReAlLy tHiNk tHaT'S A GoOd iDeA?"
Useful for arguing online or replying all to that email that accidentally
went to the whole company.
@tlancon
tlancon / us_states_dict.py
Last active May 13, 2022
Dictionary of All US States and their Abbreviations
View us_states_dict.py
# Inspired by https://gist.github.com/JeffPaine/3083347
# Access full state names using us_states.keys()
# Access all state abbreviations using us_states.values()
us_states = {
'Alabama': 'AL',
'Alaska': 'AK',
'Arizona': 'AZ',
'Arkansas': 'AR',
'California': 'CA',
'Colorado': 'CO',
@tlancon
tlancon / GetLabelAnalysisCellContents.py
Created Jul 20, 2018
Retrieves the contents of a specific cell from a tablelike-object (HxLabelAnalysis, HxSpreadSheet, etc.) in Amira/Avizo.
View GetLabelAnalysisCellContents.py
# Copy/paste into the Avizo/Amira Python console.
# Alternatively, save to a file, add that file to your path, and import.
# See docstring for usage.
def get_cell_contents(tablelike_object,row,column,table=0):
"""
Retrieves contents of cell i,j in a table through
HxSpreadSheetInterface.
You must use the object handle, not just the name of the object! For example,
to get the contents of row 4 from column 5 of a HxLabelAnalysis data object