changing log import method

docs/notebooks/.ipynb_checkpoints/Logging-checkpoint.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "ae2a75fe",
+   "metadata": {},
+   "source": [
+    "# Logging system for qim3d\n",
+    "\n",
+    "Using proper logging instead of print statements is a recommended practice.\n",
+    "\n",
+    "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. \n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "a31b2245",
+   "metadata": {
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "import qim3d\n",
+    "from qim3d.io.logger import log"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "94022824",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "warning level message\n",
+      "error level message\n",
+      "critical level message\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Here we test by sending one message for each level\n",
+    "# Note that DEBUG and INFO do not appear\n",
+    "log.debug('debug level message')\n",
+    "log.info('info level message')\n",
+    "log.warning('warning level message')\n",
+    "log.error('error level message')\n",
+    "log.critical('critical level message')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "b0856333",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "debug level message\n",
+      "info level message\n",
+      "warning level message\n",
+      "error level message\n",
+      "critical level message\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Change the level to debug\n",
+    "qim3d.io.logger.set_level_DEBUG()\n",
+    "\n",
+    "# Now all the levels get logged\n",
+    "log.debug('debug level message')\n",
+    "log.info('info level message')\n",
+    "log.warning('warning level message')\n",
+    "log.error('error level message')\n",
+    "log.critical('critical level message')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "eb542404",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "error level message\n",
+      "critical level message\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Change the level to error\n",
+    "qim3d.io.logger.set_level_ERROR()\n",
+    "\n",
+    "# And now only above ERROR is shown\n",
+    "log.debug('debug level message')\n",
+    "log.info('info level message')\n",
+    "log.warning('warning level message')\n",
+    "log.error('error level message')\n",
+    "log.critical('critical level message')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "af3cc812",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "ERROR     3224913348.py:8    error level message\n",
+      "CRITICAL  3224913348.py:9    critical level message\n"
+     ]
+    }
+   ],
+   "source": [
+    "# We can increase the level of detail\n",
+    "qim3d.io.logger.set_detailed_output()\n",
+    "\n",
+    "# Note that DEBUG and INFO are still not shown\n",
+    "log.debug('debug level message')\n",
+    "log.info('info level message')\n",
+    "log.warning('warning level message')\n",
+    "log.error('error level message')\n",
+    "log.critical('critical level message')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "d7239b1b",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "error level message\n",
+      "critical level message\n"
+     ]
+    }
+   ],
+   "source": [
+    "# We can switch back to the simple output mode\n",
+    "qim3d.io.logger.set_simple_output()\n",
+    "\n",
+    "# Now we see all the levels on simple mode\n",
+    "log.debug('debug level message')\n",
+    "log.info('info level message')\n",
+    "log.warning('warning level message')\n",
+    "log.error('error level message')\n",
+    "log.critical('critical level message')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "eaceb5b6",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "DEBUG     4221232047.py:5    debug level message\n",
+      "INFO      4221232047.py:6    info level message\n",
+      "WARNING   4221232047.py:7    warning level message\n",
+      "ERROR     4221232047.py:8    error level message\n",
+      "CRITICAL  4221232047.py:9    critical level message\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Change back to detailed and DEBUG level\n",
+    "qim3d.io.logger.set_detailed_output()\n",
+    "qim3d.io.logger.set_level_DEBUG()\n",
+    "\n",
+    "log.debug('debug level message')\n",
+    "log.info('info level message')\n",
+    "log.warning('warning level message')\n",
+    "log.error('error level message')\n",
+    "log.critical('critical level message')"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/notebooks/Logging.ipynb

@@ -25,7 +25,7 @@
    "outputs": [],
    "source": [
     "import qim3d\n",
-    "from qim3d import log"
+    "from qim3d.io.logger import log"
    ]
   },
   {

qim3d/__init__.py

@@ -3,8 +3,3 @@ import qim3d.gui
 import qim3d.tools
 import logging
 
-
-# create the logger
-log = logging.getLogger(__name__)
-qim3d.io.logger.set_simple_output()
-qim3d.io.logger.set_level_WARNING()
\ No newline at end of file

qim3d/gui/data_explorer.py

@@ -3,7 +3,7 @@ import numpy as np
 import os
 from qim3d.tools import internal_tools
 from qim3d.io import DataLoader
-from qim3d import log
+from qim3d.io.logger import log
 import tifffile
 import outputformat as ouf
 import datetime

qim3d/gui/iso3d.py

@@ -3,7 +3,7 @@ import numpy as np
 import os
 from qim3d.tools import internal_tools
 from qim3d.io import DataLoader
-from qim3d import log
+from qim3d.io.logger import log
 import plotly.graph_objects as go
 from scipy import ndimage
 

qim3d/gui/local_thickness.py

@@ -3,7 +3,7 @@ import numpy as np
 import os
 from qim3d.tools import internal_tools
 from qim3d.io import DataLoader
-from qim3d import log
+from qim3d.io.logger import log
 import tifffile
 import plotly.express as px
 from scipy import ndimage

qim3d/io/load.py

@@ -6,13 +6,13 @@ import difflib
 
 class DataLoader:
     def __init__(self, **kwargs):
-        self.verbose = False
 
         # Virtual stack is False by default
         self.virtual_stack = kwargs.get("virtual_stack", False)
 
     def load_tiff(self, path):
         if self.virtual_stack:
+            log.info("Using virtual stack")
             vol = tifffile.memmap(path)
         else:
             vol = tifffile.imread(path)

qim3d/io/logger.py

@@ -39,3 +39,10 @@ def set_level_ERROR():
 
 def set_level_CRITICAL():
     logging.getLogger("qim3d").setLevel(logging.CRITICAL)
+
+
+
+# create the logger
+log = logging.getLogger("qim3d")
+set_simple_output()
+set_level_WARNING()