Add google forms and banner

README.md

@@ -1,9 +1,11 @@
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
 # The Image Analysis Field Guide
 
-A [Jupyter Book] website 
+Essential toolkit to get started in scientific image analysis.
 
-👉 See the live website at [this URL](https://EPFL-Center-for-Imaging.github.io/image-analysis-field-guide/).
+👉 See the live website at [this URL](https://epfl-center-for-imaging.github.io/image-analysis-field-guide/).
+
+-------------------------
 
 ## Installation
 

src/README.md

@@ -12,6 +12,7 @@ New to image analysis? These short guides will help you start off on the right f
 
 - [🐍 Setting up Python for scientific image analysis](./sections/getting_started/pages/python_setup.md)
 - [🚩 Starting a new image analysis project](./sections/getting_started/pages/new_project.md)
+- More to come!
 
 ## 🚀 Starter packs
 
@@ -63,6 +64,8 @@ Performance optimization
 ```
 ````
 
+Want to add a Starter Pack? See [Contribute](#🤝-contribute).
+
 ## 📚 Exploring further
 
 Browse our collections of online resources, python examples, and software tools related to image analysis.
@@ -81,9 +84,7 @@ Browse our collections of online resources, python examples, and software tools
 
 ## 🤝 Contribute
 
-Please check out our [Contributor's guide](https://github.com/MalloryWittwer/image-analysis-field-guide/blob/main/contribute.md) to learn more about the many ways to contribute to our project.
-
-We’d be happy to receive your suggestions and to know more about the topics you are interested in!
+Please check out our [Contributor's guide](https://github.com/MalloryWittwer/image-analysis-field-guide/blob/main/contribute.md) to learn more about the ways to contribute to our project.
 
 ## 🖋️ Feedback
 

src/_config.yml

@@ -36,7 +36,7 @@ repository:
 # Add GitHub buttons to your book
 # See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
 html:
-  announcement: "🏗️ This site is under construction!"
+  announcement: "🏗️ [Jan 2024] This site is under construction!"
   favicon: "logo.ico"
   use_issues_button: false
   use_repository_button: true

src/helpers/__init__.py

@@ -53,17 +53,9 @@
 
 def filter_online_resources(tags: List[str]):
     df = DATAFRAME_ONLINE_RESOURCES.copy()
-
-    df["Name"] = [
-        '<a href="{}">{}</a>'.format(link, name)
-        for link, name in zip(df["Link"], df["Name"])
-    ]
-
     mask = df['Keywords'].str.contains('|'.join(tags), na=False)
     filtered_df = df[mask].copy()
-
-
-    filtered_df.drop(['Link', 'Keywords'], axis='columns', inplace=True)
+    filtered_df.drop('Keywords', axis='columns', inplace=True)
 
     return filtered_df
 
@@ -94,20 +86,8 @@ def filter_notebook_case_studies(tags: List[str]):
 
 def filter_software_tools(tags: List[str]):
     df = DATAFRAME_SOFTWARE_TOOLS.copy()
-
-    df["Software tool"] = [
-        '<a href="{}">{}</a>'.format(link, name)
-        for link, name in zip(df["Homepage"], df["Software tool"])
-    ]
-
-    df["Keywords"] = [
-        ''.join(['<button class="btn btn-light btn-xs" onclick="insertText(this)" style="padding: 1px; margin: 4px 2px; font-size: 12px;">{}</button>'.format(keyword) for keyword in [kw for kw in str(keywords).split(', ') if kw != 'nan']])
-        for keywords in df["Keywords"]
-    ]
-
     mask = df['Used for'].str.contains('|'.join(tags), na=False)
     filtered_df = df[mask].copy()
-
     filtered_df.drop(['Homepage', 'Used for'], axis='columns', inplace=True)
 
     return filtered_df

src/helpers/generate_notebook_case_studies.py

@@ -51,7 +51,7 @@ def get_notebook_case_studies_dataframe():
     """
     basedir = str(Path(__file__).parents[1] / 'sections')
     notebooks = glob.glob(f"{basedir}/**/*.ipynb", recursive=True)
-    # print(f"Found {len(notebooks)} notebooks to parse.")
+
     items = []
     for ipath in notebooks:
         ntbk = nbf.read(ipath, nbf.NO_CONVERT)
@@ -62,6 +62,8 @@ def get_notebook_case_studies_dataframe():
         items.append(parsed_info)
 
     df = pd.DataFrame(items)
+
+
 
     return df
 

src/helpers/notion_api.py

@@ -14,18 +14,47 @@ def get_online_resources_dataframe() -> pd.DataFrame:
     online_resources_data = query_notion_database(ONLINE_RESOURCES_DATABASE_ID)
     items = parse_online_resources(online_resources_data)
     df = pd.DataFrame(items)
+
+    df["Name"] = [
+        '<a href="{}">{}</a>'.format(link, name)
+        for link, name in zip(df["Link"], df["Name"])
+    ]
+
+    df.drop('Link', axis='columns', inplace=True)
+
+    df["Keywords"] = [
+        ''.join(['<button class="btn btn-light btn-xs" onclick="insertText(this)" style="padding: 1px; margin: 4px 2px; font-size: 12px;">{}</button>'.format(keyword) for keyword in [kw for kw in str(keywords).split(', ') if kw != 'nan']])
+        for keywords in df["Keywords"]
+    ]
+
     return df
 
 def get_software_tools_dataframe() -> pd.DataFrame:
     software_tools_data = query_notion_database(SOFTWARE_TOOLS_DATABASE_ID)
     items = parse_software_tools(software_tools_data)
     df = pd.DataFrame(items)
+
+    df["Software tool"] = [
+        '<a href="{}">{}</a>'.format(link, name)
+        for link, name in zip(df["Homepage"], df["Software tool"])
+    ]
+
+    df.drop(['Homepage'], axis='columns', inplace=True)
+
+    df["Used for"] = [
+        ''.join(['<button class="btn btn-light btn-xs" onclick="insertText(this)" style="padding: 1px; margin: 4px 2px; font-size: 12px;">{}</button>'.format(keyword) for keyword in [kw for kw in str(keywords).split(', ') if kw != 'nan']])
+        for keywords in df["Used for"]
+    ]
+
+    df["Keywords"] = [
+        ''.join(['<button class="btn btn-light btn-xs" onclick="insertText(this)" style="padding: 1px; margin: 4px 2px; font-size: 12px;">{}</button>'.format(keyword) for keyword in [kw for kw in str(keywords).split(', ') if kw != 'nan']])
+        for keywords in df["Keywords"]
+    ]
+
     return df
 
 def parse_online_resources(data: dict) -> List[dict]:
-    """
-    Extract useful data from the raw Notion database contents.
-    """
+    """Extract data from the raw Notion database contents."""
     items = []
 
     for page_contents in data.get('results'):
@@ -44,7 +73,7 @@ def parse_online_resources(data: dict) -> List[dict]:
 
 def parse_software_tools(data: dict) -> List[dict]:
     """
-    Extract useful data from the raw Notion database contents.
+    Extract data from the raw Notion database contents.
     """
     items = []
 

src/sections/exploring_further/notebook_case_studies/page.md

@@ -14,21 +14,28 @@ kernelspec:
 
 Browse our collection of Jupyter notebooks to learn more about scientific image processing and analysis in Python.
 
+````{admonition} Launch the notebooks
+Launch the notebooks to run them interactively on our `Jupyter Hub` by clicking on the rocket icon (🚀) at the top of this page (only EPFL).
+```{image} ../../../images/jupyterhub.png
+:align: center
+```
+````
+
 ```{code-cell} ipython3
 :tags: [remove-input]
 
-import pandas as pd
 from itables import init_notebook_mode
-from itables import show
-from pathlib import Path
 
 init_notebook_mode(all_interactive=True, connected=True)
 
 import sys
+from pathlib import Path
+
 sys.path.append(str(Path.cwd().parents[2]))
-from helpers import DATAFRAME_NOTEBOOK_CASE_STUDIES
+
+from helpers import DATAFRAME_NOTEBOOK_CASE_STUDIES, show_notebook_case_studies
+
 df = DATAFRAME_NOTEBOOK_CASE_STUDIES.copy()
-# df = pd.read_csv(Path.cwd().parents[3] / 'db' / 'notebook_case_studies.csv')
 
 df["Title"] = [
     '<a href="./notebooks/{}">{}</a>'.format(link, name)
@@ -40,15 +47,7 @@ df["Image"] = [
     for image in df["Image"]
 ]
 
-df.drop(['Link', 'Keywords'], axis='columns', inplace=True)
-
-show(
-    df,
-    classes="display compact", 
-    columnDefs=[
-        {"className": "dt-left", "targets": [0, 1]}
-    ],
-    paging=False,
-    showIndex=False,
-)
+df.drop(['Link', 'Keywords', 'Description'], axis='columns', inplace=True)
+
+show_notebook_case_studies(df)
 ```

src/sections/exploring_further/online_resources/page.md

@@ -21,40 +21,15 @@ Do you want to add a resource to our list? Fill-in our [Google Form](https://doc
 ```{code-cell} ipython3
 :tags: [remove-input]
 
-import pandas as pd
 from itables import init_notebook_mode
-from itables import show
-from pathlib import Path
-
 init_notebook_mode(all_interactive=True, connected=True)
 
 import sys
+from pathlib import Path
+
 sys.path.append(str(Path.cwd().parents[2]))
-from helpers import DATAFRAME_ONLINE_RESOURCES
-df = DATAFRAME_ONLINE_RESOURCES.copy()
-# df = pd.read_csv(Path.cwd().parents[3] / 'db' / 'online_resources.csv')
-
-df["Name"] = [
-    '<a href="{}">{}</a>'.format(link, name)
-    for link, name in zip(df["Link"], df["Name"])
-]
-
-df.drop('Link', axis='columns', inplace=True)
-
-df["Keywords"] = [
-    ''.join(['<button class="btn btn-light btn-xs" onclick="insertText(this)" style="padding: 1px; margin: 4px 2px; font-size: 12px;">{}</button>'.format(keyword) for keyword in [kw for kw in str(keywords).split(', ') if kw != 'nan']])
-    for keywords in df["Keywords"]
-]
-
-# show(df, classes="display compact", paging=False)
-show(
-    df,
-    classes="display compact", 
-    columnDefs=[
-        {"className": "dt-left", "targets": "_all"}
-    ],
-    style="width:100%;margin:auto",
-    paging=False,
-    showIndex=False,
-)
+
+from helpers import DATAFRAME_ONLINE_RESOURCES, show_online_resources
+
+show_online_resources(DATAFRAME_ONLINE_RESOURCES)
 ```

src/sections/exploring_further/software_tools/page.md

@@ -21,44 +21,16 @@ Do you want to add a software tool to our list? Fill-in our [Google Form](https:
 ```{code-cell} ipython3
 :tags: [remove-input]
 
-import pandas as pd
 from itables import init_notebook_mode
-from itables import show
-from pathlib import Path
 
 init_notebook_mode(all_interactive=True, connected=True)
 
 import sys
-sys.path.append(str(Path.cwd().parents[2]))
-from helpers import DATAFRAME_SOFTWARE_TOOLS
-df = DATAFRAME_SOFTWARE_TOOLS.copy()
-# df = pd.read_csv(Path.cwd().parents[3] / 'db' / 'software_tools.csv')
-
-df["Software tool"] = [
-    '<a href="{}">{}</a>'.format(link, name)
-    for link, name in zip(df["Homepage"], df["Software tool"])
-]
-
-df.drop(['Homepage'], axis='columns', inplace=True)
+from pathlib import Path
 
-df["Used for"] = [
-    ''.join(['<button class="btn btn-light btn-xs" onclick="insertText(this)" style="padding: 1px; margin: 4px 2px; font-size: 12px;">{}</button>'.format(keyword) for keyword in [kw for kw in str(keywords).split(', ') if kw != 'nan']])
-    for keywords in df["Used for"]
-]
+sys.path.append(str(Path.cwd().parents[2]))
 
-df["Keywords"] = [
-    ''.join(['<button class="btn btn-light btn-xs" onclick="insertText(this)" style="padding: 1px; margin: 4px 2px; font-size: 12px;">{}</button>'.format(keyword) for keyword in [kw for kw in str(keywords).split(', ') if kw != 'nan']])
-    for keywords in df["Keywords"]
-]
+from helpers import DATAFRAME_SOFTWARE_TOOLS, show_software_tools
 
-show(
-    df,
-    classes="display compact", 
-    columnDefs=[
-        {"className": "dt-left", "targets": "_all"}
-    ],
-    style="width:100%;margin:auto",
-    paging=False,
-    showIndex=False,
-)
+show_software_tools(DATAFRAME_SOFTWARE_TOOLS)
 ```