Commit b7a50608 authored by Francisco Romero's avatar Francisco Romero

add gif for nose and for no nose

parent c34be32a
......@@ -6,13 +6,13 @@ stored in the data generated by the tracking software [idtracker.ai](idtracker.a
The pipeline only requires the *video_object.npy* and the *blobs_collection.npy*
from [idtracker.ai](idtracker.ai) (see data folder).
The pipeline is as indicated in the following image.
For blobs that look like fish (head with lower curvarture than tail). We also have a class *FishContour* that detects the nose, and tail. This points can also be included in the skeleton. In particular, the nose is used to order the points of the skeleton from the nose to the tail. This way the interpolation does not have errors when the blob is U-shaped.
![Pipeline](fishmidline/scripts/pipeline.png)
![GIF_1](fishmidline/scripts/midline_nose.gif)
For blobs that look like fish (head with lower curvarture than tail). We also have a class *FishContour* that detects the nose, head, and tail of the fish. This points can also be included in the skeleton. Adding this points makes the extraction of the midline more robust.
When the nose is not given the points of the skeleton are not ordered and the interpolation algorithm is noisy.
![Pipeline](fishmidline/scripts/pipeline_nose.png)
![GIF_2](fishmidline/scripts/midline.gif)
## Requirements
* numpy
......
# Copied from https://gist.github.com/jeanpat/5712699
import numpy as np
import mahotas as mh
......
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