From ef1cd871b2f232be5e39da0f07509f9ce51435bb Mon Sep 17 00:00:00 2001
From: Felipe Delestro Matos <fima@pop-os.localdomain>
Date: Wed, 17 May 2023 14:48:01 +0200
Subject: [PATCH] Name change to qim3d
---
README.md | 22 +++++++++++-----------
qim/__init__.py | 3 ---
qim3d/__init__.py | 3 +++
{qim => qim3d}/css/gradio.css | 0
{qim => qim3d}/gui/__init__.py | 0
{qim => qim3d}/gui/data_explorer.py | 4 ++--
{qim => qim3d}/gui/iso3d.py | 4 ++--
{qim => qim3d}/gui/local_thickness.py | 4 ++--
{qim => qim3d}/io/__init__.py | 0
{qim => qim3d}/io/load.py | 0
{qim => qim3d}/io/save.py | 0
{qim => qim3d}/tools/__init__.py | 0
{qim => qim3d}/tools/internal_tools.py | 0
setup.py | 16 ++++++++++++++--
14 files changed, 34 insertions(+), 22 deletions(-)
delete mode 100644 qim/__init__.py
create mode 100644 qim3d/__init__.py
rename {qim => qim3d}/css/gradio.css (100%)
rename {qim => qim3d}/gui/__init__.py (100%)
rename {qim => qim3d}/gui/data_explorer.py (99%)
rename {qim => qim3d}/gui/iso3d.py (99%)
rename {qim => qim3d}/gui/local_thickness.py (99%)
rename {qim => qim3d}/io/__init__.py (100%)
rename {qim => qim3d}/io/load.py (100%)
rename {qim => qim3d}/io/save.py (100%)
rename {qim => qim3d}/tools/__init__.py (100%)
rename {qim => qim3d}/tools/internal_tools.py (100%)
diff --git a/README.md b/README.md
index ceac8ac9..75c44714 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# QIM (Quantitative Imaging)
+# QIM3D (Quantitative Imaging in 3D)
QIM is a Python library for 3D quantitative imaging analysis. It provides functionality for handling data, as well as tools for visualization and analysis.
@@ -8,7 +8,7 @@ QIM is a Python library for 3D quantitative imaging analysis. It provides functi
Install using pip:
```bash
-pip install qim
+pip install qim3d
```
@@ -19,30 +19,30 @@ pip install qim
To load image data from a file, use `qim.io.load()`
```python
-import qim
+import qim3d
# Load a TIFF file
-vol = qim.io.load("path/to/file.tif")
+vol = qim3d.io.load("path/to/file.tif")
# Load a TIFF file as a virtual stack
-vol = qim.io.load("path/to/file.tif", virtual_stack=True)
+vol = qim3d.io.load("path/to/file.tif", virtual_stack=True)
```
## GUI Components
-QIM provides GUI components for interactive data exploration. The `qim.gui` module contains various classes for visualization and analysis:
+QIM provides GUI components for interactive data exploration. The `qim3d.gui` module contains various classes for visualization and analysis:
```python
-import qim
+import qim3d
-app = qim.gui.iso3d.Interface()
+app = qim3d.gui.iso3d.Interface()
app.launch()
```
Graphical interfaces currently available:
-- Data exploration tool (`qim.gui.data_exploration`)
-- 3D visualization with isosurfaces (`qim.gui.iso3d`)
-- Local thickness (`qim.gui.local_thickness`)
+- Data exploration tool (`qim3d.gui.data_exploration`)
+- 3D visualization with isosurfaces (`qim3d.gui.iso3d`)
+- Local thickness (`qim3d.gui.local_thickness`)
diff --git a/qim/__init__.py b/qim/__init__.py
deleted file mode 100644
index e942e4db..00000000
--- a/qim/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-import qim.io
-import qim.gui
-import qim.tools
\ No newline at end of file
diff --git a/qim3d/__init__.py b/qim3d/__init__.py
new file mode 100644
index 00000000..7906a460
--- /dev/null
+++ b/qim3d/__init__.py
@@ -0,0 +1,3 @@
+import qim3d.io
+import qim3d.gui
+import qim3d.tools
\ No newline at end of file
diff --git a/qim/css/gradio.css b/qim3d/css/gradio.css
similarity index 100%
rename from qim/css/gradio.css
rename to qim3d/css/gradio.css
diff --git a/qim/gui/__init__.py b/qim3d/gui/__init__.py
similarity index 100%
rename from qim/gui/__init__.py
rename to qim3d/gui/__init__.py
diff --git a/qim/gui/data_explorer.py b/qim3d/gui/data_explorer.py
similarity index 99%
rename from qim/gui/data_explorer.py
rename to qim3d/gui/data_explorer.py
index 74208a84..94da2b0b 100644
--- a/qim/gui/data_explorer.py
+++ b/qim3d/gui/data_explorer.py
@@ -1,8 +1,8 @@
import gradio as gr
import numpy as np
import os
-from qim.tools import internal_tools
-from qim.io import DataLoader
+from qim3d.tools import internal_tools
+from qim3d.io import DataLoader
import tifffile
import outputformat as ouf
import datetime
diff --git a/qim/gui/iso3d.py b/qim3d/gui/iso3d.py
similarity index 99%
rename from qim/gui/iso3d.py
rename to qim3d/gui/iso3d.py
index 977ff6b1..5930c337 100644
--- a/qim/gui/iso3d.py
+++ b/qim3d/gui/iso3d.py
@@ -1,8 +1,8 @@
import gradio as gr
import numpy as np
import os
-from qim.tools import internal_tools
-from qim.io import DataLoader
+from qim3d.tools import internal_tools
+from qim3d.io import DataLoader
import plotly.graph_objects as go
from scipy import ndimage
diff --git a/qim/gui/local_thickness.py b/qim3d/gui/local_thickness.py
similarity index 99%
rename from qim/gui/local_thickness.py
rename to qim3d/gui/local_thickness.py
index 5ab83c11..7ff7aa74 100644
--- a/qim/gui/local_thickness.py
+++ b/qim3d/gui/local_thickness.py
@@ -1,8 +1,8 @@
import gradio as gr
import numpy as np
import os
-from qim.tools import internal_tools
-from qim.io import DataLoader
+from qim3d.tools import internal_tools
+from qim3d.io import DataLoader
import tifffile
import plotly.express as px
from scipy import ndimage
diff --git a/qim/io/__init__.py b/qim3d/io/__init__.py
similarity index 100%
rename from qim/io/__init__.py
rename to qim3d/io/__init__.py
diff --git a/qim/io/load.py b/qim3d/io/load.py
similarity index 100%
rename from qim/io/load.py
rename to qim3d/io/load.py
diff --git a/qim/io/save.py b/qim3d/io/save.py
similarity index 100%
rename from qim/io/save.py
rename to qim3d/io/save.py
diff --git a/qim/tools/__init__.py b/qim3d/tools/__init__.py
similarity index 100%
rename from qim/tools/__init__.py
rename to qim3d/tools/__init__.py
diff --git a/qim/tools/internal_tools.py b/qim3d/tools/internal_tools.py
similarity index 100%
rename from qim/tools/internal_tools.py
rename to qim3d/tools/internal_tools.py
diff --git a/setup.py b/setup.py
index 91b3958e..41ac4d58 100644
--- a/setup.py
+++ b/setup.py
@@ -1,11 +1,14 @@
from setuptools import setup, find_packages
+import os
+
# Read the contents of your README file
with open("README.md", "r", encoding="utf-8") as f:
long_description = f.read()
+
setup(
- name="qim",
+ name="qim3d",
version="0.1.0",
author="Felipe Delestro",
author_email="fima@dtu.dk",
@@ -27,5 +30,14 @@ setup(
"Topic :: Software Development :: User Interfaces",
],
python_requires=">=3.6",
- install_requires=open("requirements.txt").readlines(),
+ install_requires=['gradio>=3.31.0',
+ 'h5py>=3.8.0',
+ 'localthickness>=0.1.2',
+ 'matplotlib>=3.7.1',
+ 'numpy>=1.24.3',
+ 'outputformat>=0.1.3',
+ 'plotly>=5.14.1',
+ 'scipy>=1.10.1',
+ 'setuptools>=59.6.0',
+ 'tifffile>=2023.4.12']
)
--
GitLab