diff --git a/docs/notebooks/.ipynb_checkpoints/Logging-checkpoint.ipynb b/docs/notebooks/.ipynb_checkpoints/Logging-checkpoint.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..f5f70327dd168af03ed0fbc60efc762872271e63
--- /dev/null
+++ b/docs/notebooks/.ipynb_checkpoints/Logging-checkpoint.ipynb
@@ -0,0 +1,220 @@
+{
+ "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
+}
diff --git a/docs/notebooks/Logging.ipynb b/docs/notebooks/Logging.ipynb
index e88aa9aa413d771987614bb850d34fd00dcf9437..f5f70327dd168af03ed0fbc60efc762872271e63 100644
--- a/docs/notebooks/Logging.ipynb
+++ b/docs/notebooks/Logging.ipynb
@@ -25,7 +25,7 @@
"outputs": [],
"source": [
"import qim3d\n",
- "from qim3d import log"
+ "from qim3d.io.logger import log"
]
},
{
diff --git a/qim3d/__init__.py b/qim3d/__init__.py
index 52c04ab353f95df7e0ef7b22f5d850f29ead3ba2..87f2e56bcdf35575e4ca389348502825e6b6dd07 100644
--- a/qim3d/__init__.py
+++ b/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
diff --git a/qim3d/gui/data_explorer.py b/qim3d/gui/data_explorer.py
index 425ecfb82e457a861bd22e48b4cac762091d096b..0fa53af66707cc549e538f9cb1b1015b1098ca7f 100644
--- a/qim3d/gui/data_explorer.py
+++ b/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
diff --git a/qim3d/gui/iso3d.py b/qim3d/gui/iso3d.py
index 904a6ed474c2c46333ccabbc8a9e6266990a4a74..5e1571913d9897243d685e1f38ca8753b3a509c8 100644
--- a/qim3d/gui/iso3d.py
+++ b/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
diff --git a/qim3d/gui/local_thickness.py b/qim3d/gui/local_thickness.py
index d56430147f176bf6aa1841687449210da0bf8c3a..5107b0ecf61aa32c11bda47f084723471d0ab8f5 100644
--- a/qim3d/gui/local_thickness.py
+++ b/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
diff --git a/qim3d/io/load.py b/qim3d/io/load.py
index 8ed2ec90d09dc187f007d3d9af9ade24fa9a406f..3c6a8bfe0f42174ece09cca4c298433a67fb7aea 100644
--- a/qim3d/io/load.py
+++ b/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)
diff --git a/qim3d/io/logger.py b/qim3d/io/logger.py
index 4e7013a178fcfb14ee66bf60cc0605f4317bc5f8..d81774feb633bc61b8556c6b0300a4ed6b80de39 100644
--- a/qim3d/io/logger.py
+++ b/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()