Image edge detection

[Dipankar Ganguly]

I am trying to do an image edge detection project using Python 3.5 under Jupyter on Anaconda's Navigator on my Mac running OS 10.11.6. I have verified that  the Envirnoment does have scikit-image installed   I have run into this at the very outset.

_________________

 File "<ipython-input-8-59ade0051fc5>", line 1
    import scikit-image as image
                 ^
SyntaxError: invalid syntax

__________________

How do I solve this? Is there a more recent package I should be using?

Thanks.

Dipu

[Stéfan van der Walt]

Hi Dipu

Please try one of the examples from the gallery:

http://scikit-image.org/docs/dev/auto_examples/

Stéfan

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[Dipankar “Dipu” Ganguly]

Thank you Stefan. That was very helpful. 

I now need to convert “.jpg" and DICOM images into arrays that I can operate on using numpy and other Scikit-image algorithms/tools. What tools/packages could I use for the conversions (Images —> numpy arrays)?

Best.

Dipu

Dipankar Ganguly
Consultant: Strategy/Technology/Commercialization
Bothell, WA
Cell: 408-203-8814
email: dip...@gmail.com
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[Stéfan van der Walt]

Hi Dipu

On 9 August 2016 at 08:35, Dipankar “Dipu” Ganguly <dip...@gmail.com> wrote:

I now need to convert “.jpg" and DICOM images into arrays that I can operate on using numpy and other Scikit-image algorithms/tools. What tools/packages could I use for the conversions (Images —> numpy arrays)?

You can use pydicom to load the DICOM images to numpy arrays:

http://pydicom.readthedocs.io/en/stable/working_with_pixel_data.html

Thereafter, scikit-image can process them:

http://scikit-image.org/docs/stable/user_guide/numpy_images.html

If you have more advanced DICOM needs, such as working with multiple slices, or reading meta-data, you may want to look at dcmstack and nibabel as well.

Best regards

Stéfan

[Dipankar “Dipu” Ganguly]

Thanks again Stefa. Very helpful. I will try using these. I am assuming, I will also find tools to read .jpg images as numpy arrays, my immediate need.

Dipu

Dipankar “Dipu” Ganguly

dip...@gmail.com

Cell: 408-203-8814

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[Stéfan van der Walt]

Hi Dipu

On 9 August 2016 at 14:30, Dipankar “Dipu” Ganguly <dip...@gmail.com> wrote:

Thanks again Stefa. Very helpful. I will try using these. I am assuming, I will also find tools to read .jpg images as numpy arrays, my immediate need.

You assume correctly :)  If you take a look at the user guide I mentioned earlier, you will find examples of how to do that.

from skimage import io

image = io.imread('my_image.jpg')

Best regards

Stéfan

[Dipankar “Dipu” Ganguly]

Hi Stefan:

Sorry to bother you again. I am having trouble with "from skimage import xyz” commands. I am using Python 3.5 with Jupyter from Navigator. I am wondering if I am running into version mismatches.

Thanks.

Dipu

Dipankar “Dipu” Ganguly

dip...@gmail.com

Cell: 408-203-8814

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[Stéfan van der Walt]

Hi Dipu

On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly <dip...@gmail.com> wrote:

Sorry to bother you again. I am having trouble with "from skimage import xyz” commands. I am using Python 3.5 with Jupyter from Navigator. I am wondering if I am running into version mismatches.

Yes, I am afraid we don't have an xyz submodule.

Perhaps you can share some code with us, along with the error messages you are seeing?

Stéfan

[Dipankar “Dipu” Ganguly]

Your suggestions have been very helpful and allowed me to make good progress.

Do you know where I can find the Python source code for the edge filters in MatPlotlib?

Thanks.

Dipu

Dipankar Ganguly
Consultant: Strategy/Technology/Commercialization
Bothell, WA
Cell: 408-203-8814
email: dip...@gmail.com
http://www.linkedin.com/in/dipugee 

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[Dipankar “Dipu” Ganguly]

Hi:

I have ImageJ installed on the same Mac that I am using to develop IPython Image Processing algorithms under Anaconda Navigator’s Jupyter. Can I load ImageJ as a package in my Image Processing environment and call its functions as I do with Scikit-image?

Thanks

Dipu

Dipankar “Dipu” Ganguly

dip...@gmail.com

Cell: 408-203-8814

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[Dipankar “Dipu” Ganguly]

Hi Stefan:

I need to bug you again. I have a couple of new questions…

1 My Python 3.5 code now includes Sci-Image, numpy and matplotlib functions as well some openCV calls. I need too convert this using JPython. How easily will  these SciPy and openCV functions convert?

2. How close are SciImage and openCV in function content? Is there a document where I can find openCV equivalents to Sciimage functions and vice versa?

Thanks.

Dipu

Dipankar Ganguly
Consultant: Strategy/Technology/Commercialization
Bothell, WA
Cell: 408-203-8814
email: dip...@gmail.com
http://www.linkedin.com/in/dipugee 

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[Juan Nunez-Iglesias]

Hi Dipu,

1. I assume you mean Jython. Most of the SciPy stack is not available for Jython, unless things have changed dramatically since I last looked at it…

2. I am not aware of a document translating between scikit-image and openCV. I suspect there is substantial non-overlap. Python bindings for both should operate on numpy arrays, so I think you should use both, wherever it makes sense? Though, as mentioned above, you will have more trouble with this using Jython…

Juan.

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[Dipankar “Dipu” Ganguly]

Thanks for the quick response Juan.

Sorry. I DID mean Jython. The real issue is porting this hybrid Scikit-image/openCV/Python 3.5 code on to an Android tablet as an app. I am not an expert on that Android environment but thought Java was the common development platform. If there are other ways to accomplish that, I am all ears!

Thanks.

Dipu

 

Dipankar “Dipu” Ganguly

dip...@gmail.com

Cell: 408-203-8814

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