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Trevor Lancon tlancon

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tlancon / AutoAdjustOrthoSliceColormap.tcl
Created May 2, 2018
Auto-adjusts the colormap for Avizo/Amira Ortho Slice modules
View AutoAdjustOrthoSliceColormap.tcl
# 1. Copy/paste this into Avizo/Amira console
# 2. Select one or more Ortho Slices to auto-adjust and press F3
# Note: Can change 'onKeyFX' to the desired keybinding
proc onKeyF3 {} {
foreach slice [all -selected HxOrthoSlice] {
$slice colormap adjustRange; $slice fire
}
}
@tlancon
tlancon / CompareTwoDatasets.tcl
Last active Jun 11, 2018
Compares to selected datasets in Amira/Avizo
View CompareTwoDatasets.tcl
# 1. Copy/paste this into Avizo/Amira console
# 2. Select two datasets to compare and press Shift+F3
# Note: Can change 'onKeyFX' to the desired keybinding
# Note: Requires Avizo (not Avizo Lite) or the XImagePAQ extension for Amira
proc onKeyShiftF3 {} {
if {[llength [all -selected]] != 2} {
echo "Please select two data objects."
} else {
set before [lindex [all -selected] 0]
set after [lindex [all -selected] 1]
@tlancon
tlancon / LabelAnalysisToDataFrame.py
Created Jun 11, 2018
Converts HxLabelAnalysis or HxSpreadSheet objects to Pandas data frames in Amira/Avizo.
View LabelAnalysisToDataFrame.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 labelanalysis_to_dataframe(tablelike_object):
"""
Converts a tablelike object (HxSpreadSheet, HxLabelAnalysis, or anything with
.all_interfaces.HxSpreadSheetInterface) to a Pandas data frame with the column names intact.
You must use the object handle, not just the name of the object! For example,
to convert a HxLabelAnalysis data object named "chocolate-bar.Label-Analysis":
@tlancon
tlancon / MultipleChoice.py
Created Jun 24, 2018
Compares a user's input to a list of allowable reponses and returns the keyword.
View MultipleChoice.py
def parse_response(multiple_choice, prompt=None):
"""
Splits a user's input into individual words and searches a list
of allowable responses for a unique match, then returns the word
that matches one of the options.
List comprehension syntax explained for my own reference:
1. for i in response.split() - breaks every word of response
into individual strings
2. if i in multiple_choice - searches for ALL recognized words
@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
@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 / 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 / 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 / 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 / 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'