Notebook unit testing

Notion task: https://www.notion.so/qim-dtu/Unit-test-for-notebooks-184bab83b2f980df8b99ebb8c4386c83

• Updated the notebooks to comply with the refactoring changes.
• Implemented unit tests for all notebooks (except annotation_tool.ipynb, segmentation_pipeline.ipynb, and Unet.ipynb). The unit tests are located in qim3d/tests/notebooks/test_notebooks.py.

docs/notebooks/Logging.ipynb

 %% Cell type:markdown id:ae2a75fe tags:
 
 # Logging system for qim3d
 
 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
+from qim3d.utils._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
+# Note that DEBUG does 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
 
+    info level message
     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")
+qim3d.utils._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")
+qim3d.utils._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:75af4473 tags:
 
+``` python
+# Change the level back to info
+qim3d.utils._logger.level("info")
+
+# And now only above INFO is shown again
+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
 
+    info level message
+    warning level message
+    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()
+qim3d.utils._logger.set_detailed_output()
 
-# Note that DEBUG and INFO are still not shown
+# Note that DEBUG is 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
+    INFO      20327955.py:6    info level message
+    WARNING   20327955.py:7    warning level message
+    ERROR     20327955.py:8    error level message
+    CRITICAL  20327955.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()
+qim3d.utils._logger.set_simple_output()
 
-# Now we see all the levels on simple mode
+# Now the levels are back to 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
 
+    info level message
+    warning level message
     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")
+qim3d.utils._logger.set_detailed_output()
+qim3d.utils._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
+    DEBUG     3380703693.py:5    debug level message
+    INFO      3380703693.py:6    info level message
+    WARNING   3380703693.py:7    warning level message
+    ERROR     3380703693.py:8    error level message
+    CRITICAL  3380703693.py:9    critical level message