Add jupyter notebooks for code instruction (#72)

* Exclude notebooks from packages in `pyproject.toml` * Add notebook * Add current directory to top of the notebook for relative paths * Add to notebook * Change comment in pyproject.toml since tests are automatically excluded with flat layout * Add tutorials to README * Add `MultipleDicotPipeline` tutorial * Add `DicotPipeline` tutorial * Add `OlderMonocotPipeline` tutorial * Add `YoungerMonocotPipeline` tutorial * Add descriptions of each pipeline to notebooks * Add group property to series docstring * Update README * Update README.md Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * Update README.md Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * Update README.md Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * Update README.md Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * Update sleap_roots/series.py Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> * Fix `Series` docstring --------- Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
talmolab · Apr 4, 2024 · 4091d71 · 4091d71
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diff --git a/README.md b/README.md
@@ -30,8 +30,9 @@ import sleap_roots as sr
 
 plant = sr.Series.load(
     "tests/data/canola_7do/919QDUH.h5",
-    primary_name="primary_multi_day",
-    lateral_name="lateral_3_nodes"
+    # Specify the names of the primary and lateral roots for trait calculation
+    primary_name="primary",
+    lateral_name="lateral"
 )
 pipeline = sr.DicotPipeline()
 traits = pipeline.compute_plant_traits(plant, write_csv=True)
@@ -46,8 +47,9 @@ plant_paths = sr.find_all_series("tests/data/soy_6do")
 plants = [
     sr.Series.load(
         plant_path,
-        primary_name="primary_multi_day",
-        lateral_name="lateral__nodes",
+        # Specify the names of the primary and lateral roots for trait calculation
+        primary_name="primary",
+        lateral_name="lateral",
     ) for plant_path in plant_paths]
 
 pipeline = sr.DicotPipeline()
@@ -59,15 +61,20 @@ all_traits = pipeline.compute_batch_traits(plants, write_csv=True)
 ```py
 import sleap_roots as sr
 import numpy as np
+import numpy as np
+# Import utility for combining primary and lateral root points
+from sleap_roots.points import get_all_pts_array
 
 plant = sr.Series.load(
     "tests/data/canola_7do/919QDUH.h5",
-    primary_name="primary_multi_day",
-    lateral_name="lateral_3_nodes"
+    primary_name="primary",
+    lateral_name="lateral"
 )
 
-primary, lateral = plant[10]
-pts = np.concatenate([primary.numpy(), lateral.numpy()], axis=0).reshape(-1, 2)
+frame_index = 0
+primary_pts = plant.get_primary_points(frame_index)
+lateral_pts = plant.get_lateral_points(frame_index)
+pts = get_all_pts_array(primary_pts, lateral_pts)
 convex_hull = sr.convhull.get_convhull(pts)
 ```
 
@@ -80,8 +87,8 @@ import sleap_roots as sr
 
 plant = sr.Series.load(
     "tests/data/rice_3do/0K9E8BI.h5",
-    primary_name="longest_3do_6nodes",
-    lateral_name="main_3do_6nodes"
+    primary_name="primary",
+    lateral_name="crown"
 )
 pipeline = sr.YoungerMonocotPipeline()
 traits = pipeline.compute_plant_traits(plant, write_csv=True)
@@ -96,8 +103,8 @@ plant_paths = sr.find_all_series("tests/data/rice_3do")
 plants = [
     sr.Series.load(
         plant_path,
-        primary_name="longest_3do_6nodes",
-        lateral_name="main_3do_6nodes"
+        primary_name="primary",
+        lateral_name="crown"
     ) for plant_path in plant_paths]
 
 pipeline = sr.YoungerMonocotPipeline()
@@ -109,18 +116,42 @@ all_traits = pipeline.compute_batch_traits(plants, write_csv=True)
 ```py
 import sleap_roots as sr
 import numpy as np
+from sleap_roots.points import get_all_pts_array
 
 plant = sr.Series.load(
     "tests/data/rice_3do/0K9E8BI.h5",
-    primary_name="longest_3do_6nodes",
-    lateral_name="main_3do_6nodes"
+    primary_name="primary",
+    lateral_name="crown"
 )
 
-primary, lateral = plant[10]
-pts = np.concatenate([primary.numpy(), lateral.numpy()], axis=0).reshape(-1, 2)
+frame_index = 0
+primary_pts = plant.get_primary_points(frame_index)
+lateral_pts = plant.get_lateral_points(frame_index)
+pts = get_all_pts_array(primary_pts, lateral_pts)
 convex_hull = sr.convhull.get_convhull(pts)
 ```
 
+## Tutorials
+Jupyter notebooks are located in this repo at `sleap-roots/notebooks`.
+
+To use them, add Jupyter Lab to your conda environment (recommended):
+
+```
+conda activate sleap-roots
+pip install jupyterlab
+```
+
+Then you can change directories to the location of the notebooks, and open Jupyter Lab:
+
+```
+cd notebooks
+jupyter lab
+```
+
+Go through the commands in the notebooks to learn about each pipeline. 
+You can use the test data located at `tests/data` or copy the notebooks elsewhere for use with your own data!
+
+
 ## Development
 For development, first clone the repository:
 ```
@@ -167,4 +198,6 @@ This repository was created by the [Talmo Lab](https://talmolab.org) and [Busch
 
 ### Citation
 
-*Coming soon.*
+E.M. Berrigan, L. Wang, H. Carrillo, K. Echegoyen, M. Kappes, J. Torres, A. Ai-Perreira, E. McCoy, E. Shane, C.D. Copeland, L. Ragel, C. Georgousakis, S. Lee, D. Reynolds,    
+A. Talgo, J. Gonzalez, L. Zhang, A.B. Rajurkar, M. Ruiz, E. Daniels, L. Maree, S. Pariyar, W. Busch, T.D. Pereira. "Fast and Efficient Root Phenotyping via Pose Estimation"     
+*Plant Phenomics* 0: DOI:[10.34133/plantphenomics.0175](https://doi.org/10.34133/plantphenomics.0175).
diff --git a/notebooks/DicotPipeline.ipynb b/notebooks/DicotPipeline.ipynb
diff --git a/notebooks/MultipleDicotPipeline.ipynb b/notebooks/MultipleDicotPipeline.ipynb
diff --git a/notebooks/OlderMonocotPipeline.ipynb b/notebooks/OlderMonocotPipeline.ipynb
diff --git a/notebooks/YoungerMonocotPipeline.ipynb b/notebooks/YoungerMonocotPipeline.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -35,6 +35,11 @@ dynamic = ["version", "readme"]
 version = {attr = "sleap_roots.__version__"}
 readme = {file = ["README.md"], content-type="text/markdown"}
 
+[tool.setuptools.packages.find]
+include = ["sleap_roots"]  # Include only the sleap_roots package
+exclude = ["notebooks"]  # Exclude the notebooks directory
+namespaces = false
+
 [project.optional-dependencies]
 dev = [
     "pytest",

diff --git a/sleap_roots/series.py b/sleap_roots/series.py
@@ -38,6 +38,7 @@ class Series:
     Properties:
         series_name: Name of the series derived from the HDF5 filename.
         expected_count: Fetch the expected plant count for this series from the CSV.
+        group: Group name for the series from the CSV.
     """
 
     h5_path: Optional[str] = None