Re: Image edge detection

[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
dipu...@gmail.com
Cell: 408-203-8814







> On Sep 21, 2016, at 10:49 PM, Juan Nunez-Iglesias  wrote:
> 
> 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.
> 
> On 22 September 2016 at 2:34:12 pm, Dipankar “Dipu” Ganguly 
> (dipu...@gmail.com ) wrote:
> 
>> 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: dipu...@gmail.com 
>> http://www.linkedin.com/in/dipugee  
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>> On Aug 9, 2016, at 2:42 PM, Stéfan van der Walt >> > wrote:
>>> 
>>> Hi Dipu
>>> 
>>> On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly >> > 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
>>> 
>>> --
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Re: Image edge detection

[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.

On 22 September 2016 at 2:34:12 pm, Dipankar “Dipu” Ganguly (
dipu...@gmail.com) wrote:

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: dipu...@gmail.com
http://www.linkedin.com/in/dipugee









On Aug 9, 2016, at 2:42 PM, Stéfan van der Walt 
wrote:

Hi Dipu

On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly 
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

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Re: Image edge detection

[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: dipu...@gmail.com
http://www.linkedin.com/in/dipugee 









> On Aug 9, 2016, at 2:42 PM, Stéfan van der Walt  wrote:
> 
> Hi Dipu
> 
> On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly  > 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
> 
> -- 
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Re: Image edge detection

[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
dipu...@gmail.com
Cell: 408-203-8814







> On Aug 8, 2016, at 5:24 PM, Stéfan van der Walt  wrote:
> 
> Hi Dipu
> 
> Please try one of the examples from the gallery:
> 
> http://scikit-image.org/docs/dev/auto_examples/ 
> <http://scikit-image.org/docs/dev/auto_examples/>
> 
> Stéfan
> 
> On 8 August 2016 at 17:09, Dipankar Ganguly  <mailto:dipu...@gmail.com>> wrote:
> 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 "", 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
> 
> 
> 
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Re: Image edge detection

[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
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> On Aug 9, 2016, at 2:42 PM, Stéfan van der Walt  wrote:
> 
> Hi Dipu
> 
> On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly  > 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
> 
> -- 
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Re: Image edge detection

[Stéfan van der Walt]

Hi Dipu

On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly 
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

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Re: Image edge detection

[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
dipu...@gmail.com
Cell: 408-203-8814







> On Aug 9, 2016, at 2:34 PM, Stéfan van der Walt  wrote:
> 
> Hi Dipu
> 
> On 9 August 2016 at 14:30, Dipankar “Dipu” Ganguly  > 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
> 
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Re: Image edge detection

[Stéfan van der Walt]

Hi Dipu

On 9 August 2016 at 14:30, Dipankar “Dipu” Ganguly 
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

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Re: Image edge detection

[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
dipu...@gmail.com
Cell: 408-203-8814







> On Aug 9, 2016, at 11:40 AM, Stéfan van der Walt  wrote:
> 
> Hi Dipu
> 
> On 9 August 2016 at 08:35, Dipankar “Dipu” Ganguly  > 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
> 
> 
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Re: Image edge detection

[Stéfan van der Walt]

Hi Dipu

On 9 August 2016 at 08:35, Dipankar “Dipu” Ganguly 
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

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Re: Image edge detection

[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: dipu...@gmail.com
http://www.linkedin.com/in/dipugee 









> On Aug 8, 2016, at 5:24 PM, Stéfan van der Walt  wrote:
> 
> Hi Dipu
> 
> Please try one of the examples from the gallery:
> 
> http://scikit-image.org/docs/dev/auto_examples/ 
> <http://scikit-image.org/docs/dev/auto_examples/>
> 
> Stéfan
> 
> On 8 August 2016 at 17:09, Dipankar Ganguly  <mailto:dipu...@gmail.com>> wrote:
> 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 "", 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
> 
> 
> 
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Re: Image edge detection

[Stéfan van der Walt]

Hi Dipu

Please try one of the examples from the gallery:

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

Stéfan

On 8 August 2016 at 17:09, Dipankar Ganguly  wrote:

> 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 "", line 1import scikit-image as image
>  ^SyntaxError: invalid syntax
>
> __
>
>
> How do I solve this? Is there a more recent package I should be using?
>
>
> Thanks.
>
>
> Dipu
>
>
>
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> You received this message because you are subscribed to the Google Groups
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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 "", line 1import scikit-image as image
 ^SyntaxError: invalid syntax

__


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


Thanks.


Dipu



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