| Name | hdf5view JSON |
| Version |
0.0.7
JSON |
| download |
| home_page | |
| Summary | HDF5View is a python based HDF5 file viewer built on PyQt5/PySide2/PyQt6/PySide6, QtPy, h5py and pyqtgraph. |
| upload_time | 2023-04-17 14:21:57 |
| maintainer | Thomas G. Woodcock |
| docs_url | None |
| author | Martin Swarbrick, Thomas G. Woodcock |
| requires_python | >=3.6 |
| license | MIT License Copyright (c) 2019 Martin Swarbrick Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
research
data
management
visualization
hdf5
viewer
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://pypi.python.org/pypi/hdf5view/)
[](https://pypi.python.org/pypi/hdf5view/)
# hdf5view
Simple Qt/Python based viewer for HDF5 files. Displays a file tree, data tables and attributes and can render greyscale images of any nodes which have two or more dimensions, and rgb or rgba images of any nodes with three or more dimensions. Everything is loaded dynamically, so hopefully it should be able to handle HDF5 files of any size and structure.
## 1. Installing
#### Qt API Bindings
One of [pyqt5](https://www.riverbankcomputing.com/software/pyqt/), [pyside2](https://pyside.org), [pyqt6](https://www.riverbankcomputing.com/software/pyqt/) or [pyside6](https://pyside.org) is required in order to be able to run hdf5view. Please install one of these e.g. with pip:
```
pip install pyqt5
```
or on linux (Ubuntu/Debian), you can install a system package:
```
sudo apt install python3-pyqt5
```
[qtpy](https://github.com/spyder-ide/qtpy) is used as an abstraction layer for pyqt5/pyside2/pyqt6/pyside6. If you have any of these Qt API bindings installed, qtpy will take the first available one in the order shown in the previous sentence. hdf5view works with all of the bindings. If you have more than one of the bindings installed and want to specify which one should be used for hdf5view, you can do this by setting the `QT_API` environment variable before running hdf5view.
For example: if you have pyqt5 and pyside2 installed and you want hdf5view to use PySide2, on Windows PowerShell:
```
$env:QT_API = 'pyside2'
```
or on linux (Ubuntu/Debian)
```
export QT_API=pyside2
```
before running HDF5View
#### Other Dependencies
The other dependencies are [qtpy](https://github.com/spyder-ide/qtpy), [h5py](https://www.h5py.org/) and [pyqtgraph](https://www.pyqtgraph.org/). Currently installed versions of these dependencies will not be overwritten by installing hdf5view. If these are not already present on your system, they will be installed during the installation of hdf5view.
If you prefer to install them in advance, you can use pip:
```
pip install h5py, qtpy, pyqtgraph
```
or on linux to install system packages:
```
sudo apt install python3-h5py python3-pyqtgraph python3-qtpy
```
Note: [pyqtgraph](https://www.pyqtgraph.org/) 0.12 supports all of pyqt5, pyside2, pyqt6 or pyside6. Older versions of pyqtgraph may not support all of them.
#### hdf5view
To install the current release from PyPI system-wide on Windows:
```
pip install hdf5view
```
or on linux:
```
sudo pip3 install hdf5view
```
To install the current development version, download or clone the repo and install either system-wide on Windows:
```
cd hdf5view
pip install .
```
or on linux:
```
cd hdf5view
sudo pip3 install .
```
You could also use the flag -e with the pip command to install in editable mode, then you can pull changes from the repo and they are automatically available on your system.
To setup an isolated development environment using virtualenv:
```
python3 -m virtualenv -p python3 .
source bin/activate
pip install -e .
```
To uninstall hdf5view:
```
pip uninstall hdf5view
```
or:
```
sudo pip3 uninstall hdf5view
```
## 2. Running
From the terminal:
```
hdf5view
```
or
```
hdf5view -f <hdf5file>
```
HDF5 files can also be dropped onto the application window once opened.
You can also create a desktop link to start the program for convenience. A Windows icon file hdf5view.ico is provided in the folder hdf5view/resources/images.
## 3. Usage
The structure of the HDF5 file can be navigated using the tree view on the left hand side. The central panel displays a table of the data at the node selected. If the node has more than two dimensions, a 2D slice of the data is displayed in the table. On the right hand side you can see and modify the slice shown; and see details of the node and any associated attributes.
To display an image of a particular node, click the image icon on the toolbar at the top of the window. This will open an Image tab at the current node. You can have several image tabs open at once. Image tabs remember the node and slice if you switch to a different tab and back. Switching to a different node results in the default rendering behaviour for the image. The defaut image rendering is as follows:
* Greyscale: if the node has two or more dimensions and the shape of the last dimension is greater than 4. The image is initially taken from the last two dimensions of the node. A scrollbar is provided, which currently can be used to scroll through the first dimension of the node. This is useful for viewing a stack of greyscale images. You can alternatively change the slice manually and the scrollbar will move accordingly.
* rgb or rgba: if the node has three or more dimensions and the shape of the last dimension is three or four. If the node has more than three dimensions, a scrollbar is provided, which can be used to scroll through the first dimension. This is useful for a stack of rgb or rgba images, for example.
## 4. Testing
Currently there are no unit tests for this package. The gui has been tested with qtpy=2.2.0, pyqtgraph=0.12.4 and h5py=3.7.0 in combination with pyqt5=5.15.7, pyside2=5.15.2.1, pyqt6=6.3.1 and pyside6=6.3.2, and it works with all of the Qt API bindings.
## 5. Issues
If there are any issues, please feel free to use the [issues mechanism on github](https://github.com/marts/hdf5view/issues) to get in touch.
## TODO:
* Add xy plots in pyqtgraph
* Add a more complex slice view/delegate
* Add some 3D stuff
Raw data
{
"_id": null,
"home_page": "",
"name": "hdf5view",
"maintainer": "Thomas G. Woodcock",
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": "",
"keywords": "research,data,management,visualization,hdf5,viewer",
"author": "Martin Swarbrick, Thomas G. Woodcock",
"author_email": "",
"download_url": "https://files.pythonhosted.org/packages/17/18/0d7d46e7b55c6ee8d012ad41c7420b149e1d05f921d6803224a1d5b8f18a/hdf5view-0.0.7.tar.gz",
"platform": null,
"description": "[](https://pypi.python.org/pypi/hdf5view/)\r\n[](https://pypi.python.org/pypi/hdf5view/)\r\n\r\n# hdf5view\r\n\r\nSimple Qt/Python based viewer for HDF5 files. Displays a file tree, data tables and attributes and can render greyscale images of any nodes which have two or more dimensions, and rgb or rgba images of any nodes with three or more dimensions. Everything is loaded dynamically, so hopefully it should be able to handle HDF5 files of any size and structure.\r\n\r\n\r\n## 1. Installing\r\n\r\n#### Qt API Bindings\r\n\r\nOne of [pyqt5](https://www.riverbankcomputing.com/software/pyqt/), [pyside2](https://pyside.org), [pyqt6](https://www.riverbankcomputing.com/software/pyqt/) or [pyside6](https://pyside.org) is required in order to be able to run hdf5view. Please install one of these e.g. with pip:\r\n\r\n```\r\npip install pyqt5\r\n```\r\n\r\nor on linux (Ubuntu/Debian), you can install a system package:\r\n\r\n```\r\nsudo apt install python3-pyqt5\r\n```\r\n\r\n[qtpy](https://github.com/spyder-ide/qtpy) is used as an abstraction layer for pyqt5/pyside2/pyqt6/pyside6. If you have any of these Qt API bindings installed, qtpy will take the first available one in the order shown in the previous sentence. hdf5view works with all of the bindings. If you have more than one of the bindings installed and want to specify which one should be used for hdf5view, you can do this by setting the `QT_API` environment variable before running hdf5view.\r\n\r\nFor example: if you have pyqt5 and pyside2 installed and you want hdf5view to use PySide2, on Windows PowerShell:\r\n\r\n```\r\n$env:QT_API = 'pyside2'\r\n```\r\n\r\nor on linux (Ubuntu/Debian)\r\n\r\n```\r\nexport QT_API=pyside2\r\n```\r\n\r\nbefore running HDF5View\r\n\r\n\r\n#### Other Dependencies\r\n\r\nThe other dependencies are [qtpy](https://github.com/spyder-ide/qtpy), [h5py](https://www.h5py.org/) and [pyqtgraph](https://www.pyqtgraph.org/). Currently installed versions of these dependencies will not be overwritten by installing hdf5view. If these are not already present on your system, they will be installed during the installation of hdf5view. \r\n\r\nIf you prefer to install them in advance, you can use pip:\r\n\r\n```\r\npip install h5py, qtpy, pyqtgraph\r\n```\r\n\r\nor on linux to install system packages:\r\n\r\n```\r\nsudo apt install python3-h5py python3-pyqtgraph python3-qtpy\r\n```\r\n\r\nNote: [pyqtgraph](https://www.pyqtgraph.org/) 0.12 supports all of pyqt5, pyside2, pyqt6 or pyside6. Older versions of pyqtgraph may not support all of them.\r\n\r\n\r\n#### hdf5view\r\n\r\nTo install the current release from PyPI system-wide on Windows:\r\n\r\n```\r\npip install hdf5view\r\n```\r\n\r\nor on linux:\r\n\r\n```\r\nsudo pip3 install hdf5view\r\n```\r\n\r\nTo install the current development version, download or clone the repo and install either system-wide on Windows:\r\n\r\n```\r\ncd hdf5view\r\npip install .\r\n```\r\n\r\nor on linux:\r\n\r\n```\r\ncd hdf5view\r\nsudo pip3 install .\r\n```\r\n\r\nYou could also use the flag -e with the pip command to install in editable mode, then you can pull changes from the repo and they are automatically available on your system.\r\n\r\nTo setup an isolated development environment using virtualenv:\r\n\r\n```\r\npython3 -m virtualenv -p python3 .\r\nsource bin/activate\r\npip install -e .\r\n```\r\n\r\nTo uninstall hdf5view:\r\n\r\n```\r\npip uninstall hdf5view\r\n```\r\n\r\nor:\r\n\r\n```\r\nsudo pip3 uninstall hdf5view\r\n```\r\n\r\n## 2. Running\r\n\r\nFrom the terminal:\r\n\r\n```\r\nhdf5view\r\n```\r\n\r\nor\r\n\r\n```\r\nhdf5view -f <hdf5file>\r\n```\r\n\r\nHDF5 files can also be dropped onto the application window once opened.\r\n\r\nYou can also create a desktop link to start the program for convenience. A Windows icon file hdf5view.ico is provided in the folder hdf5view/resources/images.\r\n\r\n## 3. Usage\r\n\r\nThe structure of the HDF5 file can be navigated using the tree view on the left hand side. The central panel displays a table of the data at the node selected. If the node has more than two dimensions, a 2D slice of the data is displayed in the table. On the right hand side you can see and modify the slice shown; and see details of the node and any associated attributes.\r\n\r\nTo display an image of a particular node, click the image icon on the toolbar at the top of the window. This will open an Image tab at the current node. You can have several image tabs open at once. Image tabs remember the node and slice if you switch to a different tab and back. Switching to a different node results in the default rendering behaviour for the image. The defaut image rendering is as follows: \r\n\r\n* Greyscale: if the node has two or more dimensions and the shape of the last dimension is greater than 4. The image is initially taken from the last two dimensions of the node. A scrollbar is provided, which currently can be used to scroll through the first dimension of the node. This is useful for viewing a stack of greyscale images. You can alternatively change the slice manually and the scrollbar will move accordingly.\r\n\r\n* rgb or rgba: if the node has three or more dimensions and the shape of the last dimension is three or four. If the node has more than three dimensions, a scrollbar is provided, which can be used to scroll through the first dimension. This is useful for a stack of rgb or rgba images, for example.\r\n\r\n## 4. Testing\r\n\r\nCurrently there are no unit tests for this package. The gui has been tested with qtpy=2.2.0, pyqtgraph=0.12.4 and h5py=3.7.0 in combination with pyqt5=5.15.7, pyside2=5.15.2.1, pyqt6=6.3.1 and pyside6=6.3.2, and it works with all of the Qt API bindings.\r\n\r\n## 5. Issues\r\n\r\nIf there are any issues, please feel free to use the [issues mechanism on github](https://github.com/marts/hdf5view/issues) to get in touch.\r\n\r\n## TODO:\r\n\r\n* Add xy plots in pyqtgraph\r\n* Add a more complex slice view/delegate\r\n* Add some 3D stuff\r\n",
"bugtrack_url": null,
"license": "MIT License Copyright (c) 2019 Martin Swarbrick Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ",
"summary": "HDF5View is a python based HDF5 file viewer built on PyQt5/PySide2/PyQt6/PySide6, QtPy, h5py and pyqtgraph.",
"version": "0.0.7",
"split_keywords": [
"research",
"data",
"management",
"visualization",
"hdf5",
"viewer"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "ed8715e5553107203191107dd9b17394286191ddc8a7d46fd295b5683481cabc",
"md5": "872c14033c0ef4664cd1ae17822143cc",
"sha256": "b42594ffd9cb78ff7f74495e8348fd8a0aef4abaf766694108395da3cd77a5df"
},
"downloads": -1,
"filename": "hdf5view-0.0.7-py3-none-any.whl",
"has_sig": false,
"md5_digest": "872c14033c0ef4664cd1ae17822143cc",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.6",
"size": 37985,
"upload_time": "2023-04-17T14:21:55",
"upload_time_iso_8601": "2023-04-17T14:21:55.299648Z",
"url": "https://files.pythonhosted.org/packages/ed/87/15e5553107203191107dd9b17394286191ddc8a7d46fd295b5683481cabc/hdf5view-0.0.7-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "17180d7d46e7b55c6ee8d012ad41c7420b149e1d05f921d6803224a1d5b8f18a",
"md5": "abd52c5ddc037e79447568dd1e152088",
"sha256": "54d2974614b512c98f58e94e9e49d97b4cdd4d2afd47a87e227e42af044e270b"
},
"downloads": -1,
"filename": "hdf5view-0.0.7.tar.gz",
"has_sig": false,
"md5_digest": "abd52c5ddc037e79447568dd1e152088",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 37721,
"upload_time": "2023-04-17T14:21:57",
"upload_time_iso_8601": "2023-04-17T14:21:57.511585Z",
"url": "https://files.pythonhosted.org/packages/17/18/0d7d46e7b55c6ee8d012ad41c7420b149e1d05f921d6803224a1d5b8f18a/hdf5view-0.0.7.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-04-17 14:21:57",
"github": false,
"gitlab": false,
"bitbucket": false,
"lcname": "hdf5view"
}
