amine0110/pycad

Welcome to PYCAD, a comprehensive library designed to simplify and streamline medical imaging tasks. From data preprocessing to advanced visualization, PYCAD empowers professionals, researchers, and enthusiasts to harness the power of modern algorithms and techniques with ease.

Installation

1. Clone the repository:

   pip install pycad-medic

For more installation instructions, please see this.

Features & Usage

• Image File Conversion: Between NIFTI and DICOM formats.
• Visualization: Upcoming feature to visualize medical imaging data.
• Data Preprocessing: Including data splitting and annotation conversion.
• Dataset Creation: Configurations for YOLOv8.

For detailed usage and examples, refer to the tutorials directory and documentation.

What is New?

The latest release contains some new exciting features, if you want to know more about the new features you can read the release features documentation.

Contributions & Support

We value contributions from the community! If you find a bug, want to propose a feature, or simply have a question, feel free to open an issue on our GitHub repository.

For deeper insights and support, consider booking a premium session with us.

License

PYCAD is licensed under the MIT License. See the LICENSE file for more details.

Connect with Us

Stay updated with our latest advancements:

• 📹 YouTube
• 📖 Blog
• 📧 Newsletter
• 💼 Premium Sessions

Contact & Inquiries

For business inquiries, please reach out to us at:

📧 [email protected]

---

Visitor count

pycad's Issues

SimpleITK :ERROR: vector dimension mismatch

Hi,
I have encountered issue connected with converting nifiti to dicom using NiftiToDicomConverter. An error was raised in SimpleITK. I tried to convert one of the files from the Decathlon project, precisely BRATS_002 which is a file containing a brain image. The same problem occurs with converting most of nifit files. Has somebody encountered similar problem?
Here is a full stacktrace:
File "c:\User\nifiti_to_dicom_v2\main.py", line 6, in <module> converter.nifti2dicom_1file(in_dir, out_dir) File "c:\User\nifiti_to_dicom_v2\pycad\pycad\converters\nifti_to_dicom.py", line 95, in nifti2dicom_1file list(map(lambda i: self.writeSlices(series_tag_values, new_img, i, out_dir), range(new_img.GetDepth()))) File "c:\User\nifiti_to_dicom_v2\pycad\pycad\converters\nifti_to_dicom.py", line 95, in <lambda> list(map(lambda i: self.writeSlices(series_tag_values, new_img, i, out_dir), range(new_img.GetDepth()))) File "c:\User\nifiti_to_dicom_v2\pycad\pycad\converters\nifti_to_dicom.py", line 62, in writeSlices image_slice.SetMetaData("0020|0032", '\\'.join(map(str,new_img.TransformIndexToPhysicalPoint((0,0,i))))) # Image Position (Patient) File "C:\User\AppData\Local\Programs\Python\Python39\lib\site-packages\SimpleITK\SimpleITK.py", line 3266, in TransformIndexToPhysicalPoint return _SimpleITK.Image_TransformIndexToPhysicalPoint(self, index) RuntimeError: Exception thrown in SimpleITK Image_TransformIndexToPhysicalPoint: D:\a\1\sitk\Code\Common\src\sitkPimpleImageBase.hxx:246: sitk::ERROR: vector dimension mismatch

error "install pycad-medic"

Dear Mohammed,

I have tried to install it using: !pip install pycad-medic, but I got error like this:

WARNING: This is not valid Python code. If you want to use IPython magics, flexible indentation, and prompt removal, we recommend that you save this file with the .ipy extension.

Collecting pycad-medic
Downloading pycad_medic-0.0.10-py3-none-any.whl (246 kB)
Collecting tqdm==4.66.1
Using cached tqdm-4.66.1-py3-none-any.whl (78 kB)
Requirement already satisfied: glob2 in c:\users\asus\anaconda3\envs\py37gpu\lib\site-packages (from pycad-medic) (0.7)
Collecting gdown==4.7.1
ERROR: Cannot install pycad-medic==0.0.10, pycad-medic==0.0.3, pycad-medic==0.0.4, pycad-medic==0.0.5, pycad-medic==0.0.6, pycad-medic==0.0.7, pycad-medic==0.0.8 and pycad-medic==0.0.9 because these package versions have conflicting dependencies.
Downloading gdown-4.7.1-py3-none-any.whl (15 kB)
Collecting pydicom==2.4.3
Using cached pydicom-2.4.3-py3-none-any.whl (1.8 MB)
Collecting pycad-medic
Using cached pycad_medic-0.0.9-py3-none-any.whl (244 kB)
Using cached pycad_medic-0.0.8-py3-none-any.whl (242 kB)
Using cached pycad_medic-0.0.7-py3-none-any.whl (241 kB)
Using cached pycad_medic-0.0.6-py3-none-any.whl (241 kB)
Using cached pycad_medic-0.0.5-py3-none-any.whl (37 kB)
Using cached pycad_medic-0.0.4-py3-none-any.whl (37 kB)
Using cached pycad_medic-0.0.3-py3-none-any.whl (37 kB)

The conflict is caused by:
pycad-medic 0.0.10 depends on scikit-image==0.22.0
pycad-medic 0.0.9 depends on scikit-image==0.22.0
pycad-medic 0.0.8 depends on scikit-learn==1.1.2
pycad-medic 0.0.7 depends on scikit-learn==1.1.2
pycad-medic 0.0.6 depends on scikit-learn==1.1.2
pycad-medic 0.0.5 depends on scikit-learn==1.1.2
pycad-medic 0.0.4 depends on scikit-learn==1.1.2
pycad-medic 0.0.3 depends on scikit-learn==1.1.2

To fix this you could try to:

1. loosen the range of package versions you've specified
2. remove package versions to allow pip attempt to solve the dependency conflict

ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies

Own name of the output file after conversion

Hi, Mohammed.
Thank you for that modern and convenient project!

Add the ability to set your own output file name after conversion, for example DICOM series to a NRRD file. Or you can use DICOM metadata for auto naming generation.