From cdb7248ef52ee414051c0737311901d4810267e0 Mon Sep 17 00:00:00 2001
From: Jordao Bragantini <jordao.bragantini@czbiohub.org>
Date: Thu, 11 May 2023 13:56:35 -0700
Subject: [PATCH] first commit

---
 .gitignore       |  1 +
 LICENSE          | 29 +++++++++++++++++++++++++++
 README.md        | 17 ++++++++++++++++
 main.py          | 52 ++++++++++++++++++++++++++++++++++++++++++++++++
 requirements.txt |  3 +++
 5 files changed, 102 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 LICENSE
 create mode 100644 README.md
 create mode 100644 main.py
 create mode 100644 requirements.txt

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..2641667
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+*.mp4
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..85da9d3
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, Royerlab
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..cf83a20
--- /dev/null
+++ b/README.md
@@ -0,0 +1,17 @@
+# Zebrahub's `napari-animation` Demo
+
+This repository contains an example of how the videos from the zebrahub articles were rendered.
+
+## Installation
+
+```
+pip install -r requirements.txt
+```
+
+## Usage
+
+Edit the `MULTISCALE` variable inside the script to load a lower or higher resolution version of the dataset.
+
+```
+python main.py
+```
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..67fdef1
--- /dev/null
+++ b/main.py
@@ -0,0 +1,52 @@
+import napari
+from napari_animation import Animation
+
+
+def main() -> None:
+    # toggle multiscale to tradeoff between speed and resolution
+    MULTISCALE = False
+
+    viewer = napari.Viewer()
+
+    viewer.open(
+        "http://public.czbiohub.org/royerlab/zebrahub/imaging/multi-view/ZMNS001.ome.zarr",
+        plugin="napari-ome-zarr",
+        rendering="attenuated_mip",
+        gamma=0.7,
+    )
+
+    # disabling multiscale
+    if not MULTISCALE:
+        for channel in ("mezzo", "h2afva"):
+            viewer.layers[channel].multiscale = False
+            viewer.layers[channel].data = viewer.layers[channel].data[0]
+
+    # aesthetics changes
+    viewer.layers["h2afva"].colormap = "cyan"
+    viewer.layers["h2afva"].contrast_limits = (50, 850)
+    viewer.layers["mezzo"].colormap = "magenta"
+    viewer.layers["mezzo"].contrast_limits = (50, 500)
+
+    # making it 3D
+    viewer.dims.ndisplay = 3
+
+    # setting t = 0
+    viewer.dims.set_point(0, 0)
+
+    # starting recording
+    animation = Animation(viewer)
+    animation.capture_keyframe()
+
+    # setting t = 220
+    viewer.dims.set_point(0, 220)
+
+    # updating contrasts
+    viewer.layers["h2afva"].contrast_limits = (50, 2500)
+
+    # ending recording
+    animation.capture_keyframe(600)
+    animation.animate('video.mp4', fps=60)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..2316002
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,3 @@
+napari==0.4.17
+napari-animation
+napari-ome-zarr==0.5.2