Refactoring: naming of qim3d and QIM

README.md

-# Qim3D (Quantitative Imaging in 3D)
+# qim3D (Quantitative Imaging in 3D)
 
 The `qim3d` (kɪm θriː diː) library is designed to make it easier to work with 3D imaging data in Python. It offers a range of features, including data loading and manipulation, image processing and filtering, visualization of 3D data, and analysis of imaging results.
 

docs/cli.md

@@ -33,7 +33,7 @@ This offers quick interactions, making it ideal for tasks that require efficienc
 | `--anotation-tool` | Starts the annotation tool |
 | `--layers` | Starts the tool for segmenting layers |
 | `--host` | Desired host for the server. By default runs on `0.0.0.0`  |
-| `--platform` | Uses the Qim platform API for a unique path and port depending on the username |
+| `--platform` | Uses the QIM platform API for a unique path and port depending on the username |
 
 
 !!! Example

mkdocs.yml

 site_name: qim3d documentation
 site_url: https://platform.qim.dk/qim3d/
-site_author: Qim3d contributors
-site_description: Documentation for the Qim3d python library
+site_author: qim3d contributors
+site_description: Documentation for the qim3d python library
 repo_url: https://lab.compute.dtu.dk/QIM/tools/qim3d
 repo_name: Gitlab
 

qim3d/cli.py

@@ -18,7 +18,7 @@ def parse_tuple(arg):
 
 
 def main():
-    parser = argparse.ArgumentParser(description="Qim3d command-line interface.")
+    parser = argparse.ArgumentParser(description="qim3d command-line interface.")
     subparsers = parser.add_subparsers(title="Subcommands", dest="subcommand")
 
     # GUIs
@@ -167,7 +167,7 @@ def main():
 
             except qim3d.viz.NotInstalledError as err:
                 print(err)
-                message = "Itk-vtk-viewer is not installed or qim3d can not find it.\nYou can either:\n\to  Use 'qim3d viz SOURCE -m k3d' to display data using different method\n\to  Install itk-vtk-viewer yourself following https://kitware.github.io/itk-vtk-viewer/docs/cli.html#Installation\n\to  Let QIM3D install itk-vtk-viewer now (it will also install node.js in qim3d library)\nDo you want QIM3D to install itk-vtk-viewer now?"
+                message = "Itk-vtk-viewer is not installed or qim3d can not find it.\nYou can either:\n\to  Use 'qim3d viz SOURCE -m k3d' to display data using different method\n\to  Install itk-vtk-viewer yourself following https://kitware.github.io/itk-vtk-viewer/docs/cli.html#Installation\n\to  Let qim3D install itk-vtk-viewer now (it will also install node.js in qim3d library)\nDo you want qim3D to install itk-vtk-viewer now?"
                 print(message)
                 answer = input("[Y/n]:")
                 if answer in "Yy":

qim3d/gui/__init__.py

@@ -5,7 +5,7 @@ from . import iso3d
 from . import local_thickness
 from . import annotation_tool
 from . import layers2d
-from .qim_theme import QimTheme
+from .qim_theme import QIMTheme
 
 
 def run_gradio_app(gradio_interface, host="0.0.0.0"):

qim3d/gui/interface.py

@@ -57,7 +57,7 @@ class BaseInterface(ABC):
             If defined, the interface will be launched with the image already there
             This argument is used especially in jupyter notebooks, where you can launch
             interface in loop with different picture every step
-        force_light_mode: The qim platform doesn't have night mode. The qim_theme thus
+        force_light_mode: The QIM platform doesn't have night mode. The QimTheme thus
             has option to display only light mode so it corresponds with the website. Preferably
             will be removed as we add night mode to the website.
         """

qim3d/gui/qim_theme.py

@@ -2,7 +2,7 @@ import gradio as gr
 
 class QimTheme(gr.themes.Default):
     """
-    QIM3D Theme for gradio interface
+    Theme for qim3d gradio interfaces.
     The theming options are quite broad. However if there is something you can not achieve with this theme
     there is a possibility to add some more css if you override _get_css_theme function as shown at the bottom
     in comments.
@@ -12,7 +12,7 @@ class QimTheme(gr.themes.Default):
         Parameters:
         -----------
         - force_light_mode (bool, optional): Gradio themes have dark mode by default. 
-                Qim platform is not ready for dark mode yet, thus the tools should also be in light mode.
+                QIM platform is not ready for dark mode yet, thus the tools should also be in light mode.
                 This sets the darkmode values to be the same as light mode values.
         """
         super().__init__()

qim3d/utils/cli.py

@@ -2,7 +2,7 @@ import argparse
 from qim3d.gui import data_explorer, iso3d, annotation_tool, local_thickness, layers2d
 
 def main():
-    parser = argparse.ArgumentParser(description='Qim3d command-line interface.')
+    parser = argparse.ArgumentParser(description='qim3d command-line interface.')
     subparsers = parser.add_subparsers(title='Subcommands', dest='subcommand')
 
     # subcommands

qim3d/viz/itk_vtk_viewer/run.py

@@ -83,7 +83,7 @@ def itk_vtk(
     Opens a visualization window using the itk-vtk-viewer. Works both for common file types (Tiff, Nifti, etc.) and for **OME-Zarr stores**.
 
     This function starts the itk-vtk-viewer, either using a global
-    installation or a local installation within the QIM package. It also starts
+    installation or a local installation within the qim3d package. It also starts
     an HTTP server to serve the file to the viewer. Optionally, it can
     automatically open a browser window to display the viewer. If the viewer
     is not installed, it raises a NotInstalledError.