diff --git a/2 - Driftcorrection.py b/2 - Driftcorrection.py
index e49ce78..df059c6 100644
--- a/2 - Driftcorrection.py
+++ b/2 - Driftcorrection.py
@@ -97,8 +97,14 @@ def plot_stack(images, n, grid=False):
n=widgets.IntSlider(original.shape[0]//2, 0, original.shape[0]-1, 1, continuous_update=False)
)
+# Get extent, by any means necessary. Example with center and square of fftsize
+center = [dim//2 for dim in original.shape[1:]]
+extent = (center[0]-fftsize, center[0]+fftsize, center[1]-fftsize, center[1]+fftsize)
+fftsize = max(extent[1]-extent[0], extent[3]-extent[2]) //2 # used in calc half matrices
+
# Step 1 to 3 of the algorithm as described in section 4 of the paper.
-sobel = crop_and_filter(original[Eslice,...].rechunk({0:dE}), sigma=3, finalsize=2*fftsize)
+sobel = Reg.crop_and_filter_extent(original[Eslice, ...].rechunk({0: dE}), extent, sigma=sigma)
+#sobel = crop_and_filter(original[Eslice,...].rechunk({0:dE}), sigma=3, finalsize=2*fftsize)
sobel = (sobel - sobel.mean(axis=(1,2), keepdims=True)) #.persist()
sobel
diff --git a/StatRegistration_multiNLP.ipynb b/StatRegistration_multiNLP.ipynb
new file mode 100644
index 0000000..e7bce53
--- /dev/null
+++ b/StatRegistration_multiNLP.ipynb
@@ -0,0 +1,859 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "1bb538aa",
+ "metadata": {},
+ "source": [
+ "This is statregistration.py but then for multiple .nlp's. Edited from Tobias' script:\n",
+ "\n",
+ " Calculates shifts from CPcorrected and create a shift corrected stack. The calculations implements the drift\n",
+ " correction algorithm as described in section 4 of the paper.\n",
+ " https://doi.org/10.1016/j.ultramic.2019.112913\n",
+ " https://github.com/TAdeJong/LEEM-analysis/blob/master/2%20-%20Driftcorrection.ipynb\n",
+ "\n",
+ " It uses cross correlation of all pairs of\n",
+ " images after applying digital smoothing and edge detection filters to align\n",
+ " Low Energy Electron Microscopy images with each other. When applied correctly,\n",
+ " this allows for sub-pixel accurate image registration.\n",
+ "\n",
+ " Config parameters:\n",
+ " SAVEFIG, boolean whether to save the figures\n",
+ " stride: A stride larger than 1 takes 1 every stride images of the total dataset, This decreases computation time\n",
+ " by a factor of stride**2, but decreases accuracy\n",
+ " blocksize: dE is the blocksize used by dask, the number of images computed for at once.\n",
+ " fftsize: The size of the image for which the drift correction is calculated\n",
+ " startI: Starting frame for which the drift correction is calculated\n",
+ " endI: Ending frame for which the drift correction is calculated\n",
+ " sigma: the gaussian width over which the images are smoothened\n",
+ "\n",
+ "Added napari to choose a rectangular patch on which to perform drift correction."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 33,
+ "id": "52f39001",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "C:\\Users\\wgstam\\Anaconda3\\envs\\pyL5\\lib\\site-packages\\distributed\\node.py:160: UserWarning: Port 8787 is already in use.\n",
+ "Perhaps you already have a cluster running?\n",
+ "Hosting the HTTP server on port 62459 instead\n",
+ " warnings.warn(\n"
+ ]
+ },
+ {
+ "data": {
+ "text/html": [
+ "