Merge pull request #162 from jinhan/h01-interface-new

H01 interface

docs/examples/4_remote/plot_04_remote_h01.py

@@ -0,0 +1,115 @@
+"""
+H01 Dataset
+============
+
+In this notebook, you can learn how to work with the H01 dataset using Navis.
+
+The [H01 dataset](https://www.science.org/doi/10.1126/science.adk4858) contains 57,000 cells and 150 million synapses from a cubic millimeter of the human temporal cortex, which is [proofreading](https://h01-release.storage.googleapis.com/proofreading.html) in the CAVE. 
+With this interface, you can access both a snapshot of the proofread dataset and the latest dataset using CAVEclient.
+"""
+
+
+# %%
+import navis
+import navis.interfaces.h01 as h01
+
+# %%
+## Examples in using Navis interface for H01 dataset
+
+# %%
+client = h01.get_cave_client()
+
+# %%
+## Query Tables
+
+# %%
+client.materialize.get_versions()
+
+# %%
+client.materialize.get_tables()
+
+# %%
+### Query Materialized Synapse Table
+
+# %%
+client.materialize.synapse_query(limit=10)
+
+# %%
+syn = client.materialize.synapse_query(
+ post_ids=[864691131861340864],
+ # pre_ids=[ADD YOUR ROOT ID],
+)
+syn.head()
+
+# %%
+print(len(syn))
+
+# %%
+### Live Synapse Queries
+
+# %%
+import datetime
+# check if root ID is the most recent root ID
+root_id = 864691131861340864
+now = datetime.datetime.now(datetime.timezone.utc)
+is_latest = client.chunkedgraph.is_latest_roots([root_id], timestamp=now)
+latest_id = client.chunkedgraph.get_latest_roots(root_id, timestamp=now)
+print(is_latest) 
+print(latest_id)
+
+# %%
+synapse_table = client.info.get_datastack_info()['synapse_table']
+df=client.materialize.query_table(synapse_table,
+ timestamp = datetime.datetime.now(datetime.timezone.utc),
+ filter_equal_dict = {'post_pt_root_id': latest_id[0]})
+print(len(df))
+df.head()
+
+# %%
+### Query Cells Table
+
+# %%
+ct = client.materialize.query_table(table="cells")
+ct.head()
+
+# %%
+ct.cell_type.unique()
+
+# %%
+### Filter by cell type
+
+# %%
+interneuron_ids = ct[ct.cell_type == "INTERNEURON"].pt_root_id.values[:50]
+
+# %%
+interneuron_ids = interneuron_ids[interneuron_ids != 0 ]
+interneuron_ids
+
+# %%
+len(interneuron_ids)
+
+# %%
+interneurons = h01.fetch_neurons(interneuron_ids, lod=2, with_synapses=False)
+
+# %%
+interneurons_ds = navis.simplify_mesh(interneurons, F=1/3)
+
+# %%
+interneurons_ds
+
+# %%
+import seaborn as sns
+colors = {n.id: sns.color_palette('Reds', 7)[i] for i, n in enumerate(interneurons_ds)}
+fig = navis.plot3d([interneurons_ds], color=colors)
+
+# %%
+## Get Skeletons
+
+# %%
+interneurons_sk = navis.skeletonize(interneurons, parallel=True)
+
+# %%
+interneurons_sk
+
+# %%
+fig = navis.plot3d([interneurons_sk[0], interneurons[0]], color=[(1, 0, 0), (1, 1, 1, .5)])