addition of headers and some warning handling

docs/cli.md

@@ -11,6 +11,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
 
 
 ## Graphical User Interfaces
+The command line interface allows you to run graphical user interfaces directly from the terminal.
 
 ### `qim3d gui`
 !!! quote "Reference"
@@ -38,7 +39,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
 
 !!! Example
 
-    Here's an example of how to open the [Data Explorer](gui.md#data_explorer)
+    Here's an example of how to open the [Data Explorer](gui.md#qim3d.gui.data_explorer)
 
     ``` title="Command"
     qim3d gui --data-explorer
@@ -85,16 +86,6 @@ This offers quick interactions, making it ideal for tasks that require efficienc
 
 
 
-
-
-
-
-
-
-
-
-
-
 ## Data visualization
 The command line interface also allows you to easily visualize data.
 
@@ -190,7 +181,8 @@ Or an specific path for destination can be used. We can also choose to not open
     This writes to disk the `my_plot.html` file.
 
 ## File preview
-Command line interface, which allows users to preview 3D structers or 2D images directly in command line.
+File previewing can also be done directly from the command line interface to preview 3D structure or 2D images.
+
 ###  `qim3d preview`
 | Arguments | Description |
 | --------- | ----------- |

docs/io.md → docs/datahandling.md

-# Data input and output
-Dealing with volumetric data can be done by `qim3d` for the most common image formats available.
+# Data handling
+Dealing with volumetric data can be done by `qim3d` for the most common image formats available. This includes loading, saving and file conversions.
 
 Currently, it is possible to directly load `tiff`, `h5`, `nii`,`txm`, `vol` and common `PIL` formats using one single function.
 
+Additionally, synthtetic volumetric data can be generated using the `generate` module.
+
 ::: qim3d.io
     options:
         members:
-            - load
-            - load_mesh
+            - load            
             - save
-            - save_mesh
             - Downloader
             - export_ome_zarr
-            - import_ome_zarr
\ No newline at end of file
+            - import_ome_zarr
+            - save_mesh
+            - load_mesh
+
+::: qim3d.mesh
+    options:
+        members:
+            - from_volume
+
+::: qim3d.generate
+    options:
+        members:
+            - noise_object
+            - noise_object_collection

docs/detection.md

+# Detection in volumetric data
+
+The `qim3d` library provides a set of detection methods for volumes.
+
+::: qim3d.detection
+    options:
+        members:
+            - blobs
\ No newline at end of file

docs/features.md

+# Feature extraction
+
+The `qim3d` library provides a set of methods for feature extraction on volumetric data
+
+::: qim3d.features
+    options:
+        members:
+            - area
+            - volume
+            - sphericity

docs/filters.md

+# Filtering data
+
+The `qim3d` library provides a set of methods for filtering volumes.
+
+::: qim3d.filters
+    options:
+        members:
+            - gaussian
+            - median
+            - maximum
+            - minimum
+            - tophat
+
+::: qim3d.filters.Pipeline
+    options:
+        members:
+            - append
\ No newline at end of file

docs/generate.md

-# Generating synthetic data
-
-The `qim3d` library provides a set of methods for generating volumes consisting of a single synthetic blob or a collection of multiple synthetic blobs. 
-
-::: qim3d.generate
-    options:
-        members:
-            - noise_object
-            - noise_object_collection

docs/operations.md

+# Operations on volumetric data
+
+The `qim3d` library provides a set of methods for different operations on volumes.
+
+::: qim3d.operations
+    options:
+        members:
+            - remove_background
+            - fade_mask
+            - overlay_rgb_images
\ No newline at end of file

docs/processing.md

@@ -8,47 +8,4 @@ Here, we provide functionalities designed specifically for 3D image analysis and
             - structure_tensor
             - local_thickness
             - get_lines
-            - segment_layers
-
-::: qim3d.mesh
-    options:
-        members:
-            - from_volume
-
-::: qim3d.detection
-    options:
-        members:
-            - blobs
-
-::: qim3d.operations
-    options:
-        members:
-            - remove_background
-            - fade_mask
-            - overlay_rgb_images
-
-::: qim3d.segmentation
-    options:
-      members:
-        - watershed
-        - get_3d_cc
-
-::: qim3d.filters
-    options:
-        members:
-            - gaussian
-            - median
-            - maximum
-            - minimum
-            - tophat
-::: qim3d.filters.Pipeline
-    options:
-        members:
-            - append
-
-::: qim3d.features
-    options:
-        members:
-            - area
-            - volume
-            - sphericity
\ No newline at end of file
+            - segment_layers
\ No newline at end of file

docs/releases.md

@@ -7,7 +7,7 @@ Below, you'll find details about the version history of `qim3d`.
 
 As the library is still in its early development stages, **there may be breaking changes** before `v1.0` without prior deprecation warnings. Therefore, it's advisable to review the release history for more information if you encounter any issues.
 
-And remember to keep your pip installation [up to date](/qim3d/#get-the-latest-version) so that you have the latest features!
+And remember to keep your pip installation [up to date](index.md/#get-the-latest-version) so that you have the latest features!
 
 ### v0.4.5 (21/11/2024)
 

docs/segmentation.md

+# Segmenting data
+
+The `qim3d` library provides a set of methods for data segmentation.
+
+::: qim3d.segmentation
+    options:
+      members:
+        - watershed
+        - get_3d_cc

mkdocs.yml

@@ -7,14 +7,17 @@ repo_name: Gitlab
 
 
 nav:
-   
   - qim3d: index.md
-  - Input & Output: io.md
-  - Data Generation: generate.md
-  - Processing: processing.md
+  - Data handling: datahandling.md
   - Visualization: viz.md
-  - GUIs: gui.md
+  - Features: features.md
+  - Filters: filters.md
+  - Detection: detection.md
+  - Segmentation: segmentation.md
+  - Operations: operations.md
+  - Processing: processing.md
   - ML Models: models.md
+  - GUIs: gui.md
   - CLI: cli.md
 
   - Release history: releases.md

qim3d/cli/__init__.py

@@ -6,7 +6,15 @@ import qim3d
 import os
 
 QIM_TITLE = ouf.rainbow(
-    f"\n         _          _____     __ \n  ____ _(_)___ ___ |__  /____/ / \n / __ `/ / __ `__ \ /_ </ __  /  \n/ /_/ / / / / / / /__/ / /_/ /   \n\__, /_/_/ /_/ /_/____/\__,_/    \n  /_/                 v{qim3d.__version__}\n\n",
+    rf"""
+             _          _____     __ 
+      ____ _(_)___ ___ |__  /____/ / 
+     / __ `/ / __ `__ \ /_ </ __  /  
+    / /_/ / / / / / / /__/ / /_/ /   
+    \__, /_/_/ /_/ /_/____/\__,_/    
+      /_/                 v{qim3d.__version__}
+
+    """,
     return_str=True,
     cmap="hot",
 )