Additions
- Created a new class, `anumSelect`, which determines the optimum number of bins along alpha
- Created two new glasses, `graphData` and `graphSet` to handle plotting landmark data
- Created a new class `treeClassifier` which handles running the random forest classifier
- Added functions to facilitate corrections to pca alignment
- Added utility.py which contains functions that assist with manual alignment correction
Changes
- In lm.calc_bins, input is a dictionary of dfs as opposed to a list of df values from dfs.values()
- `convert_to_arr` added option for selecting r or pts datatype (`DT`)
- Added the datatype parameter required for `convert_to_arr` to the `anumSelect` functions
- `raw_data` funtion changed to select channel so that background = 1 and signal = 0 in line with expectation that pixel values function like a p value
- Correct `calc_variance` to use `np.nanvar` instead of `np.var`
- Change names to deltascope in github and folders
- Median threshold value is rescaled to accommodate 0-255 image data that is output by skimage.filters.median
- `find_r` was only calculating distance in Y and Z so added X as well
- median filter threshold in `calculate_pca_median` is set to select all points that do not have a value of 255 (background). User input signal is not used.
- Move content from old_cranium back into __init__.py
- Change documentation references to cranium to deltascope