Logging fix (#155)

* changed logging function and updated createHash func based on new ViewerState class

* cleared outputs in example notebook

* fixed logging issue in python code

* added note about Google Chrome

* type in readme

* Update README.md

added note about Safari bug in readme

README.md

@@ -132,14 +132,15 @@ 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)
 ```
-
 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). 

python/src/intracktive/convert.py

@@ -304,9 +304,9 @@ 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 = (
@@ -324,14 +324,17 @@ 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)
+    logging.info("Copy the following URL into the Google Chrome browser:")
+    logging.info("full URL: %s", fullUrl)
     webbrowser.open(fullUrl)
 
 

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

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": [

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": [