Update to Jupyter Notebook.

Signed-off-by: Jan André Reuter <jan.andre.reuter@hotmail.de>

README.md

@@ -133,7 +133,8 @@ SLIXLineplotParameterGenerator -i [INPUT-TXT-FILES] -o [OUTPUT-FOLDER] [[paramet
 | -------------- | --------------------------------------------------------------------------- |
 | `--smoothing`  | Smoothing of SLI profiles before evaluation. The smoothing is performed using a Savitzky-Golay filter with 45 sampling points and a second order polynomial. (Designed for measurements with <img src="https://render.githubusercontent.com/render/math?math=\Delta\phi"> < 5° steps to reduce the impact of irrelevant details in the fiber structure, cf. orange vs. black curve in Figure 1c in the [paper](https://github.com/3d-pli/SLIX/blob/master/paper/paper.pdf).) |
 | `--with_plots` | Generates plots (png-files) showing the SLI profiles and the determined peak positions (orange dots: before correction; green crosses: after correction). |
-| `--target_peak_height` | Change peak tip height used for correcting the peak positions. (Default: 6% of total signal amplitude). Only recommended for experienced users! |
+| `--prominence_threshold` | Change the threshold for prominent peaks. Peaks with lower prominences will not be used for further evaluation. (Default: 8% of total signal amplitude.) Only recommended for experienced users! (default: 0.08) |
+
 
 ### Example
 The following example demonstrates the evaluation of two SLI profiles, which can be found in the "examples" folder of the SLIX repository:
@@ -201,8 +202,6 @@ The following example demonstrates the generation of the parameter maps, for two
 
 <img src="https://jugit.fz-juelich.de/j.reuter/slix/-/raw/assets/Screenshot_Demo1.png" height="327">&nbsp;&nbsp;<img src="https://jugit.fz-juelich.de/j.reuter/slix/-/raw/assets/Screenshot_Demo2.png" height="327">
 
-![](https://jugit.fz-juelich.de/j.reuter/slix/-/raw/assets/demo.gif)
-
 #### How to run the demo yourself:
 
 ##### 1. Download the needed files:

examples/Visualization_Example.ipynb

@@ -529,21 +529,19 @@
     "\n",
     "```python\n",
     "from SLIX import toolbox, visualization, io\n",
-    "import nibabel\n",
-    "import numpy\n",
     "import os\n",
+    "import numpy\n",
     "\n",
     "# loop over all SLI image stacks in the folder 'input_raw'\n",
     "for file in input_raw:    \n",
     "    filename_without_extension = os.path.splitext(os.path.basename(file))[0]\n",
     "    # compute unit vector maps (UnitX, UnitY)\n",
     "    image = io.imread(file)\n",
-    "    peaks = toolbox.peaks(image)\n",
-    "    prominence_full = toolbox.peak_prominence(image, peaks)\n",
-    "    peaks[prominence_full < 0.08] = 0\n",
+    "    peaks = toolbox.significant_peaks(image)\n",
     "    centroids = toolbox.centroid_correction(image, peaks)\n",
     "    directions = toolbox.direction(peaks, centroids)\n",
     "    UnitX, UnitY = visualization.unit_vectors(directions)\n",
+    "    UnitZ = numpy.zeros(UnitX.shape)\n",
     "    # save unit vector maps as NIfTI images in the folder 'input_tract' (generate UnitZ filled with zeros)\n",
     "    io.imsave('input_tract/' + filename_without_extension + '_UnitX.nii', UnitX)\n",
     "    io.imsave('input_tract/' + filename_without_extension + '_UnitY.nii', UnitY)\n",
@@ -584,4 +582,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 1
-}
+}
\ No newline at end of file