Draft: Notebook update

https://www.notion.so/qim-dtu/v1-0-prep-Update-Notebooks-15abab83b2f9807f807fc2a381fce4d4

Not necessarily complete - would just like review and start discussion. Some notebooks are not completed due to various reasons.

docs/notebooks/Logging.ipynb

 %% Cell type:markdown id:ae2a75fe tags:
 
-# Logging system for qim3d
+# Logging system for qim3d (FOR INTERNAL USE)
 
 Using proper logging instead of print statements is a recommended practice.
 
 While print statements can be helpful for quick debugging, logging provides a more powerful and versatile approach. Logging allows for better control over output, with options to configure log levels, filter messages, and redirect output to different destinations.
 
 %% Cell type:code id:a31b2245 tags:
 
 ``` python
 import qim3d
 from qim3d.io.logger import log
 ```
 
 %% Cell type:code id:94022824 tags:
 
 ``` python
 # Here we test by sending one message for each level
 # Note that DEBUG and INFO do not appear
 log.debug('debug level message')
 log.info('info level message')
 log.warning('warning level message')
 log.error('error level message')
 log.critical('critical level message')
 ```
 
 %% Output
 
     warning level message
     error level message
     critical level message
 
 %% Cell type:code id:b0856333 tags:
 
 ``` python
 # Change the level to debug
 qim3d.io.logger.level("debug")
 
 # Now all the levels get logged
 log.debug('debug level message')
 log.info('info level message')
 log.warning('warning level message')
 log.error('error level message')
 log.critical('critical level message')
 ```
 
 %% Output
 
     debug level message
     info level message
     warning level message
     error level message
     critical level message
 
 %% Cell type:code id:eb542404 tags:
 
 ``` python
 # Change the level to error
 qim3d.io.logger.level("error")
 
 # And now only above ERROR is shown
 log.debug('debug level message')
 log.info('info level message')
 log.warning('warning level message')
 log.error('error level message')
 log.critical('critical level message')
 ```
 
 %% Output
 
     error level message
     critical level message
 
 %% Cell type:code id:af3cc812 tags:
 
 ``` python
 # We can increase the level of detail
 qim3d.io.logger.set_detailed_output()
 
 # Note that DEBUG and INFO are still not shown
 log.debug('debug level message')
 log.info('info level message')
 log.warning('warning level message')
 log.error('error level message')
 log.critical('critical level message')
 ```
 
 %% Output
 
     ERROR     3224913348.py:8    error level message
     CRITICAL  3224913348.py:9    critical level message
 
 %% Cell type:code id:d7239b1b tags:
 
 ``` python
 # We can switch back to the simple output mode
 qim3d.io.logger.set_simple_output()
 
 # Now we see all the levels on simple mode
 log.debug('debug level message')
 log.info('info level message')
 log.warning('warning level message')
 log.error('error level message')
 log.critical('critical level message')
 ```
 
 %% Output
 
     error level message
     critical level message
 
 %% Cell type:code id:eaceb5b6 tags:
 
 ``` python
 # Change back to detailed and DEBUG level
 qim3d.io.logger.set_detailed_output()
 qim3d.io.logger.level("debug")
 
 log.debug('debug level message')
 log.info('info level message')
 log.warning('warning level message')
 log.error('error level message')
 log.critical('critical level message')
 ```
 
 %% Output
 
     DEBUG     1186198911.py:5    debug level message
     INFO      1186198911.py:6    info level message
     WARNING   1186198911.py:7    warning level message
     ERROR     1186198911.py:8    error level message
     CRITICAL  1186198911.py:9    critical level message