From c993ced83a6ab5170c6c02c82296f2227a8f8744 Mon Sep 17 00:00:00 2001 From: Teun Huijben Date: Mon, 16 Dec 2024 08:34:07 -0800 Subject: [PATCH 1/6] changed logging function and updated createHash func based on new ViewerState class --- python/src/intracktive/convert.py | 13 +- python/src/intracktive/createHash.py | 2 + .../notebook1_inTRACKtive_from_notebook.ipynb | 4315 ++++++++++++++++- 3 files changed, 4319 insertions(+), 11 deletions(-) diff --git a/python/src/intracktive/convert.py b/python/src/intracktive/convert.py index d17976f7..436f0d05 100644 --- a/python/src/intracktive/convert.py +++ b/python/src/intracktive/convert.py @@ -1,7 +1,6 @@ import logging import tempfile import time -import webbrowser from pathlib import Path from typing import Iterable @@ -304,9 +303,9 @@ def dataframe_to_browser(df: pd.DataFrame, zarr_dir: Path) -> None: if str(zarr_dir) in (".", None): with tempfile.TemporaryDirectory() as temp_dir: zarr_dir = Path(temp_dir) - logging.info("Temporary directory used for localhost:", zarr_dir) + logging.info("Temporary directory used for localhost: %s", zarr_dir) else: - logging.info("Provided directory used used for localhost:", zarr_dir) + logging.info("Provided directory used used for localhost: %s", zarr_dir) extra_cols = [] zarr_path = ( @@ -324,15 +323,17 @@ def dataframe_to_browser(df: pd.DataFrame, zarr_dir: Path) -> None: threaded=True, ) - logging.info("localhost successfully launched, serving:", zarr_dir_with_storename) + logging.info( + "localhost successfully launched, serving: %s", zarr_dir_with_storename + ) baseUrl = "https://intracktive.sf.czbiohub.org" # inTRACKtive application dataUrl = hostURL + "/zarr_bundle.zarr/" # exact path of the data (on localhost) fullUrl = baseUrl + generate_viewer_state_hash( data_url=str(dataUrl) ) # full hash that encodes viewerState - logging.info("full URL", fullUrl) - webbrowser.open(fullUrl) + logging.info("full URL: %s", fullUrl) + # webbrowser.open(fullUrl) @click.command(name="convert") diff --git a/python/src/intracktive/createHash.py b/python/src/intracktive/createHash.py index 80af66b7..1e6390e6 100644 --- a/python/src/intracktive/createHash.py +++ b/python/src/intracktive/createHash.py @@ -32,6 +32,8 @@ def generate_viewer_state_hash(data_url: str) -> str: "showTrackHighlights": True, "cameraPosition": [-4, 0, 0], "cameraTarget": [0, 0, 0], + "pointSize": 0.1, + "trackWidthFactor": 1, } # Step 1: Serialize the viewer state to a JSON string diff --git a/python/src/intracktive/examples/notebook1_inTRACKtive_from_notebook.ipynb b/python/src/intracktive/examples/notebook1_inTRACKtive_from_notebook.ipynb index b7f6de1c..f0aff1bc 100644 --- a/python/src/intracktive/examples/notebook1_inTRACKtive_from_notebook.ipynb +++ b/python/src/intracktive/examples/notebook1_inTRACKtive_from_notebook.ipynb @@ -16,7 +16,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -34,9 +34,165 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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track_idtzyxparent_track_id
000122112333-1
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201118115333-1
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\n", + "

110899 rows × 6 columns

\n", + "
" + ], + "text/plain": [ + " track_id t z y x parent_track_id\n", + "0 0 0 122 112 333 -1\n", + "1 0 8 106 140 294 -1\n", + "2 0 1 118 115 333 -1\n", + "3 0 7 105 122 303 -1\n", + "4 0 2 119 116 331 -1\n", + "... ... ... ... ... ... ...\n", + "110894 1331 374 152 156 244 1000\n", + "110895 1331 378 147 160 233 1000\n", + "110896 1331 375 151 156 244 1000\n", + "110897 1331 377 148 159 235 1000\n", + "110898 1331 373 153 156 245 1000\n", + "\n", + "[110899 rows x 6 columns]" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "df = pd.read_csv(\"https://public.czbiohub.org/royerlab/zoo/C_elegans/tracks.csv\")\n", "df" @@ -51,9 +207,4158 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:root:Temporary directory used for localhost: /var/folders/0x/59zp_92x3dsgz9ms3l24tbsm0000gp/T/tmphvh01v0d\n", + "INFO:intracktive.convert:Munged 110899 points in 0.1783894589971169 seconds\n", + "INFO:intracktive.convert:Chased track lineage forward in 0.0006145420047687367 seconds (4 iterations)\n", + "INFO:intracktive.convert:Chased track lineage backward in 0.0009241670049959794 seconds (4 iterations)\n", + "INFO:intracktive.convert:Parsed dataframe and converted to CSR data structures in 0.036935417003405746 seconds\n", + "INFO:intracktive.convert:Saved to Zarr in 0.19353004100412363 seconds\n", + "INFO:root:Server started in background thread at http://127.0.0.1:8000\n", + "INFO:root:localhost successfully launched, serving: None\n", + "INFO:root:full URL: https://intracktive.sf.czbiohub.org#viewerState=%7B%22dataUrl%22%3A%22http%3A%2F%2F127.0.0.1%3A8000%2Fzarr_bundle.zarr%2F%22%2C%22curTime%22%3A0%2C%22minTime%22%3A-6%2C%22maxTime%22%3A5%2C%22maxPointsPerTimepoint%22%3A0%2C%22pointBrightness%22%3A1.0%2C%22selectedPointIds%22%3A%5B%5D%2C%22showTracks%22%3Atrue%2C%22showTrackHighlights%22%3Atrue%2C%22cameraPosition%22%3A%5B-4%2C0%2C0%5D%2C%22cameraTarget%22%3A%5B0%2C0%2C0%5D%2C%22pointSize%22%3A0.1%2C%22trackWidthFactor%22%3A1%7D\n", + "INFO:root:Serving /var/folders/0x/59zp_92x3dsgz9ms3l24tbsm0000gp/T/tmphvh01v0d at http://127.0.0.1:8000\n", + "INFO:root:Server running...\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "127.0.0.1 - 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- [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/121.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/115.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/115.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/109.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/109.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/103.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/103.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/98.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/98.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/95.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/95.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - 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- [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/107.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/123.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/123.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/137.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/137.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/156.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/156.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/161.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/161.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/167.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/167.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/185.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/185.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/190.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/190.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/194.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/194.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/197.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/197.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/201.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/201.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/204.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/204.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/206.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/206.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/209.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/209.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/212.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/212.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/215.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - 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- [16/Dec/2024 08:31:40] \"GET /zarr_bundle.zarr/points/255.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:40] \"OPTIONS /zarr_bundle.zarr/points/256.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:40] \"GET /zarr_bundle.zarr/points/256.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:40] \"OPTIONS /zarr_bundle.zarr/points/257.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:40] \"GET /zarr_bundle.zarr/points/257.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:40] \"OPTIONS /zarr_bundle.zarr/points/259.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:40] \"GET /zarr_bundle.zarr/points/259.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:40] \"OPTIONS /zarr_bundle.zarr/points/260.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:40] \"GET /zarr_bundle.zarr/points/260.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - - [16/Dec/2024 08:31:41] \"OPTIONS /zarr_bundle.zarr/points/262.0 HTTP/1.1\" 200 -\n", + "127.0.0.1 - 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"execution_count": 2, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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track_idtzyxparent_track_id
000122112333-1
108106140294-1
201118115333-1
307105122303-1
402119116331-1
.....................
11089413313741521562441000
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11089813313731531562451000
\n", - "

110899 rows × 6 columns

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" - ], - "text/plain": [ - " track_id t z y x parent_track_id\n", - "0 0 0 122 112 333 -1\n", - "1 0 8 106 140 294 -1\n", - "2 0 1 118 115 333 -1\n", - "3 0 7 105 122 303 -1\n", - "4 0 2 119 116 331 -1\n", - "... ... ... ... ... ... ...\n", - "110894 1331 374 152 156 244 1000\n", - "110895 1331 378 147 160 233 1000\n", - "110896 1331 375 151 156 244 1000\n", - "110897 1331 377 148 159 235 1000\n", - "110898 1331 373 153 156 245 1000\n", - "\n", - "[110899 rows x 6 columns]" - ] - }, - "execution_count": 2, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "df = pd.read_csv(\"https://public.czbiohub.org/royerlab/zoo/C_elegans/tracks.csv\")\n", "df" @@ -207,4158 +51,9 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "INFO:root:Temporary directory used for localhost: /var/folders/0x/59zp_92x3dsgz9ms3l24tbsm0000gp/T/tmphvh01v0d\n", - "INFO:intracktive.convert:Munged 110899 points in 0.1783894589971169 seconds\n", - "INFO:intracktive.convert:Chased track lineage forward in 0.0006145420047687367 seconds (4 iterations)\n", - "INFO:intracktive.convert:Chased track lineage backward in 0.0009241670049959794 seconds (4 iterations)\n", - "INFO:intracktive.convert:Parsed dataframe and converted to CSR data structures in 0.036935417003405746 seconds\n", - "INFO:intracktive.convert:Saved to Zarr in 0.19353004100412363 seconds\n", - "INFO:root:Server started in background thread at http://127.0.0.1:8000\n", - "INFO:root:localhost successfully launched, serving: None\n", - "INFO:root:full URL: https://intracktive.sf.czbiohub.org#viewerState=%7B%22dataUrl%22%3A%22http%3A%2F%2F127.0.0.1%3A8000%2Fzarr_bundle.zarr%2F%22%2C%22curTime%22%3A0%2C%22minTime%22%3A-6%2C%22maxTime%22%3A5%2C%22maxPointsPerTimepoint%22%3A0%2C%22pointBrightness%22%3A1.0%2C%22selectedPointIds%22%3A%5B%5D%2C%22showTracks%22%3Atrue%2C%22showTrackHighlights%22%3Atrue%2C%22cameraPosition%22%3A%5B-4%2C0%2C0%5D%2C%22cameraTarget%22%3A%5B0%2C0%2C0%5D%2C%22pointSize%22%3A0.1%2C%22trackWidthFactor%22%3A1%7D\n", - 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- [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/86.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/86.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/89.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/89.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/92.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/92.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/97.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/97.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/101.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/101.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/105.0 HTTP/1.1\" 200 -\n", - 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"127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/175.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/177.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/177.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/178.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/178.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/179.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/179.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/180.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/180.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/181.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/181.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/170.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/170.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/165.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/165.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/160.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/160.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/151.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/151.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/144.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/144.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/140.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/140.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/129.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/129.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/121.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/121.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/115.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/115.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/109.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/109.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/103.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/103.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/98.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/98.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/95.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/95.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/90.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/90.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/87.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/87.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/85.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/85.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/84.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/84.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/96.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/96.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/107.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/107.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"OPTIONS /zarr_bundle.zarr/points/123.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:31:35] \"GET /zarr_bundle.zarr/points/123.0 HTTP/1.1\" 200 -\n", - 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"127.0.0.1 - - [16/Dec/2024 08:32:48] \"OPTIONS /zarr_bundle.zarr/points/346.0 HTTP/1.1\" 200 -\n", - "127.0.0.1 - - [16/Dec/2024 08:32:48] \"OPTIONS /zarr_bundle.zarr/points/343.0 HTTP/1.1\" 200 -\n" - ] - } - ], + "outputs": [], "source": [ "# Choose the location where the Zarr file will be stored, providing an empty path (Path()) means that the data will be stored in a temporary location\n", "zarr_dir = Path()\n", From 921bd5f1c2363242993942a5bd110dc5377c4bf5 Mon Sep 17 00:00:00 2001 From: TeunHuijben Date: Thu, 9 Jan 2025 12:53:15 -0800 Subject: [PATCH 3/6] fixed logging issue in python code --- python/src/intracktive/convert.py | 3 ++- .../examples/notebook2_inTRACKtive_from_napari.ipynb | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/python/src/intracktive/convert.py b/python/src/intracktive/convert.py index 436f0d05..95dad7bb 100644 --- a/python/src/intracktive/convert.py +++ b/python/src/intracktive/convert.py @@ -1,6 +1,7 @@ import logging import tempfile import time +import webbrowser from pathlib import Path from typing import Iterable @@ -333,7 +334,7 @@ def dataframe_to_browser(df: pd.DataFrame, zarr_dir: Path) -> None: data_url=str(dataUrl) ) # full hash that encodes viewerState logging.info("full URL: %s", fullUrl) - # webbrowser.open(fullUrl) + webbrowser.open(fullUrl) @click.command(name="convert") diff --git a/python/src/intracktive/examples/notebook2_inTRACKtive_from_napari.ipynb b/python/src/intracktive/examples/notebook2_inTRACKtive_from_napari.ipynb index 139831c8..bd4bcb85 100644 --- a/python/src/intracktive/examples/notebook2_inTRACKtive_from_napari.ipynb +++ b/python/src/intracktive/examples/notebook2_inTRACKtive_from_napari.ipynb @@ -17,7 +17,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -52,7 +52,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ From 9d2d6efcb117109a4bc5e545082d3afdc5e23994 Mon Sep 17 00:00:00 2001 From: TeunHuijben Date: Thu, 9 Jan 2025 13:04:27 -0800 Subject: [PATCH 4/6] added note about Google Chrome --- python/src/intracktive/convert.py | 1 + 1 file changed, 1 insertion(+) diff --git a/python/src/intracktive/convert.py b/python/src/intracktive/convert.py index 95dad7bb..efdea570 100644 --- a/python/src/intracktive/convert.py +++ b/python/src/intracktive/convert.py @@ -333,6 +333,7 @@ def dataframe_to_browser(df: pd.DataFrame, zarr_dir: Path) -> None: fullUrl = baseUrl + generate_viewer_state_hash( data_url=str(dataUrl) ) # full hash that encodes viewerState + logging.info("Copy the following URL into the Google Chrome browser:") logging.info("full URL: %s", fullUrl) webbrowser.open(fullUrl) From b132659e0f466bc7f69015368824b42fdcbc2515 Mon Sep 17 00:00:00 2001 From: TeunHuijben Date: Thu, 9 Jan 2025 13:07:39 -0800 Subject: [PATCH 5/6] type in readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3769057c..55e8a9b4 100644 --- a/README.md +++ b/README.md @@ -132,7 +132,7 @@ Open this link in the browser, navigate to the exact dataset, right-click on the ### ii) Open `inTRACKtive` using a Jupyter Notebook -To make the previous two proccesses (conversion + hosting data) easiest, we compiled them into a single python function, which is demonstration in a [Jupyter Notebook (`/napari/src/intracktive/examples`)](/python/src/intracktive/examples/notebook1_inTRACKtive_from_notebook.ipynb). +To make the previous two proccesses (conversion + hosting data) easier, we compiled them into a single python function, which is demonstration in a [Jupyter Notebook (`/napari/src/intracktive/examples`)](/python/src/intracktive/examples/notebook1_inTRACKtive_from_notebook.ipynb). ``` dataframe_to_browser(data, zarr_dir) From 8454b23217faadc0b404aab4a8bf952f75b158c0 Mon Sep 17 00:00:00 2001 From: Teun Huijben <45037215+TeunHuijben@users.noreply.github.com> Date: Thu, 9 Jan 2025 13:10:16 -0800 Subject: [PATCH 6/6] Update README.md added note about Safari bug in readme --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 55e8a9b4..d1c9f670 100644 --- a/README.md +++ b/README.md @@ -137,9 +137,10 @@ To make the previous two proccesses (conversion + hosting data) easier, we compi ``` dataframe_to_browser(data, zarr_dir) ``` - where `data` is a `pandas.dataFrame` containing the tracking data, and `zarr_dir` to directory on your computer to save the Zarr file. The `dataframe_to_browser` function, under the hood, sequentially: 1) converts pd.dataFrame to Zarr, 2) saves the Zarr in the specified location, 3) spins up a localhost at that location, and 4) launches a browser window of `inTRACKtive` with as dataUrl the zarr in the localhost. All in a function call. +> ⚠️ Currently `dataframe_to_browser` only works for Chrome and Firefox + ### iii) Open `inTRACKtive` using the napari widget Using the same capabilities of the `dataframe_to_browser`, we made a [napari](https://napari.org/stable/) widget. The widget (`intracktiveWidget`) is part of the python package after `pip install`, and automatically shows up in the napari widget list (`plugins>inTRACKtive`). To keep the `inTRACKtive` python package light-weight, napari is not listed as one of it's dependecies. To make use of the napari widget, please `pip install napari[all]` in the same conda environment as `inTRACKtive`. The widget takes the tracking data from a [`tracks`](https://napari.org/dev/howtos/layers/tracks.html) layer in napari and opens an `inTRACKtive` browser window with the data. We provide an example of how to use the widget in a [Jupyter Notebook (`/napari/src/intracktive/examples`)](/python/src/intracktive/examples/notebook2_inTRACKtive_from_napari.ipynb).