From jalopcar at gmail.com  Fri Dec  1 16:35:30 2017
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Fri, 1 Dec 2017 16:35:30 -0500
Subject: [scikit-image] my fast watershed has pass all the
 test_watershed check
In-Reply-To: <20171129190342.4A1B6AC00BB@webmail.sinamail.sina.com.cn>
References: <20171129190342.4A1B6AC00BB@webmail.sinamail.sina.com.cn>
Message-ID: <CANsMHoNPTy4Q_qz8G1=aWK_4XRq=5ZPJp7n0rGBZhK6J-hpRZA@mail.gmail.com>

Hi,

Does this script run under python 2.7 and 3.6?

Jaime

On Wed, Nov 29, 2017 at 2:03 PM, <imagepy at sina.com> wrote:

> Hi Everyone:
> I had implemented a watershed by numba, and now it has pass all the
> test_watershed check and got a exactly same result with skimage, support
> watershed-line, support connectivity, (pass test 0-12, but mine did not
> support compact yet)
>
> It support nd, now only support uint8 image with uint16 marks. (because I
> think sometimes it is enough, It can process float image if it is needed)
>
> And it is very smart and fast. less than 100 lines, and faster than
> skimage one. a 3d image which skimage run more than 10 minutes ( and I
> cannot wait any longer, so kill it), but my watershed just need 28 s.
>
> The code are attached.
>
> Best
> YXDragon
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>


-- 

*Jaime Lopez Carvajal*
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From jalopcar at gmail.com  Fri Dec  1 16:47:25 2017
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Fri, 1 Dec 2017 16:47:25 -0500
Subject: [scikit-image] my fast watershed has pass all the
 test_watershed check
In-Reply-To: <20171129190342.4A1B6AC00BB@webmail.sinamail.sina.com.cn>
References: <20171129190342.4A1B6AC00BB@webmail.sinamail.sina.com.cn>
Message-ID: <CANsMHoM-w=Efr1UsDbVM_DsdFWdVdvRrommRbKARQXruxFTBeg@mail.gmail.com>

Hi YXDragon,

The majority of tests, except 1,3,9,11, generates this error: Connectivity
dimension must be same as image

Do you think, I have an older version of skimage? or could it be another
thing?

Jaime





On Wed, Nov 29, 2017 at 2:03 PM, <imagepy at sina.com> wrote:

> Hi Everyone:
> I had implemented a watershed by numba, and now it has pass all the
> test_watershed check and got a exactly same result with skimage, support
> watershed-line, support connectivity, (pass test 0-12, but mine did not
> support compact yet)
>
> It support nd, now only support uint8 image with uint16 marks. (because I
> think sometimes it is enough, It can process float image if it is needed)
>
> And it is very smart and fast. less than 100 lines, and faster than
> skimage one. a 3d image which skimage run more than 10 minutes ( and I
> cannot wait any longer, so kill it), but my watershed just need 28 s.
>
> The code are attached.
>
> Best
> YXDragon
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>


-- 

*Jaime Lopez Carvajal*
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From imagepy at sina.com  Fri Dec  1 20:47:26 2017
From: imagepy at sina.com (imagepy at sina.com)
Date: Sat, 02 Dec 2017 09:47:26 +0800
Subject: [scikit-image] =?gbk?b?u9i4tKO6UmU6ICBteSBmYXN0IHdhdGVyc2hlZCBo?=
 =?gbk?q?as_pass_all_the_test=5Fwatershed_check?=
Message-ID: <20171202014726.D978681000EC@webmail.sinamail.sina.com.cn>

Hi Jaime:All my test are in the following format:
def test_watershed01():    data = np.array(..., np.uint8)    markers = np.array(..., np.uint16)    out1 = mywatershed(data, markers)    out2 = skwatershed(data, markers)    print(np.sum(out1-out2!=0))
every test gets a zero output, but the parameter has little diffrence with skimage.1. the image should be uint8 (then region can growing one level in one step)2. the markers should be uint16 (I change -1 of the orignal test into 1, we just need to make sure the marker order)3. connectivity only accept 1 or 2. means 4-connect or 8 connect.(6-connect, 28-connect for 3d)
for the float image, I think we can do a histogram normalrize. this means take full use of the range.then scale into 0-255, if nessesary, scale into 0-65536, then my watershed can process it.
"Connectivity dimension must be same as image" I think it is generated by scikit-image, which version  do you use?
BestYXDragon----- ???? -----
????Jaime Lopez Carvajal <jalopcar at gmail.com>
????imagepy at sina.com,  "Mailing list for scikit-image (http://scikit-image.org)" <scikit-image at python.org>
???Re: [scikit-image] my fast watershed has pass all the test_watershed check
???2017?12?02? 05?47?

Hi YXDragon,
The majority of tests, except 1,3,9,11, generates this error: Connectivity dimension must be same as image
Do you think, I have an older version of skimage? or could it be another thing?
Jaime



On Wed, Nov 29, 2017 at 2:03 PM,  <imagepy at sina.com> wrote:
Hi Everyone:I had implemented a watershed by numba, and now it has pass all the test_watershed check and got a exactly same result with skimage, support watershed-line, support connectivity, (pass test 0-12, but mine did not support compact yet)
It support nd, now only support uint8 image with uint16 marks. (because I think sometimes it is enough, It can process float image if it is needed)
And it is very smart and fast. less than 100 lines, and faster than skimage one. a 3d image which skimage run more than 10 minutes ( and I cannot wait any longer, so kill it), but my watershed just need 28 s.
The code are attached. 
BestYXDragon
_______________________________________________

scikit-image mailing list

scikit-image at python.org

https://mail.python.org/mailman/listinfo/scikit-image




-- 
Jaime Lopez Carvajal



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From jalopcar at gmail.com  Fri Dec  1 21:47:48 2017
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Fri, 1 Dec 2017 21:47:48 -0500
Subject: [scikit-image] =?utf-8?b?5Zue5aSN77yaUmU6IG15IGZhc3Qgd2F0ZXJz?=
	=?utf-8?q?hed_has_pass_all_the_test=5Fwatershed_check?=
In-Reply-To: <20171202014726.D978681000EC@webmail.sinamail.sina.com.cn>
References: <20171202014726.D978681000EC@webmail.sinamail.sina.com.cn>
Message-ID: <CANsMHoPev8s=0gZLhbvr+aSFSBFnrx66XQ59TuCSWoZFhidx2A@mail.gmail.com>

Hi YXDragon,

Thanks for your test's description, I find them very clear.
As I wrote to you, the problem only appear with tests that use the third
parameter in *skwatershed function*, because your function works fine.

>out1 = watershed(data, markers, *2*)     # works fine
>out2 = skwatershed(data, markers, *2*)  # does not work

I have installed skimage version 0.12.3 with python 2.7, maybe your code is
for python 3.5?

Jaime



On Fri, Dec 1, 2017 at 8:47 PM, <imagepy at sina.com> wrote:

> Hi Jaime:
> All my test are in the following format:
>
> def test_watershed01():
>     data = np.array(..., np.uint8)
>     markers = np.array(..., np.uint16)
>     out1 = mywatershed(data, markers)
>     out2 = skwatershed(data, markers)
>     print(np.sum(out1-out2!=0))
>
> every test gets a zero output, but the parameter has little diffrence with
> skimage.
> 1. the image should be uint8 (then region can growing one level in one
> step)
> 2. the markers should be uint16 (I change -1 of the orignal test into 1,
> we just need to make sure the marker order)
> 3. connectivity only accept 1 or 2. means 4-connect or 8
> connect.(6-connect, 28-connect for 3d)
>
> for the float image, I think we can do a histogram normalrize. this means
> take full use of the range.
> then scale into 0-255, if nessesary, scale into 0-65536, then my watershed
> can process it.
>
> "Connectivity dimension must be same as image" I think it is generated by
> scikit-image, which version  do you use?
>
> Best
> YXDragon
> ----- ???? -----
> ????Jaime Lopez Carvajal <jalopcar at gmail.com>
> ????imagepy at sina.com, "Mailing list for scikit-image (
> http://scikit-image.org)" <scikit-image at python.org>
> ???Re: [scikit-image] my fast watershed has pass all the test_watershed
> check
> ???2017?12?02? 05?47?
>
> Hi YXDragon,
>
> The majority of tests, except 1,3,9,11, generates this error: Connectivity
> dimension must be same as image
>
> Do you think, I have an older version of skimage? or could it be another
> thing?
>
> Jaime
>
>
>
>
>
> On Wed, Nov 29, 2017 at 2:03 PM, <imagepy at sina.com> wrote:
>
> Hi Everyone:
> I had implemented a watershed by numba, and now it has pass all the
> test_watershed check and got a exactly same result with skimage, support
> watershed-line, support connectivity, (pass test 0-12, but mine did not
> support compact yet)
>
> It support nd, now only support uint8 image with uint16 marks. (because I
> think sometimes it is enough, It can process float image if it is needed)
>
> And it is very smart and fast. less than 100 lines, and faster than
> skimage one. a 3d image which skimage run more than 10 minutes ( and I
> cannot wait any longer, so kill it), but my watershed just need 28 s.
>
> The code are attached.
>
> Best
> YXDragon
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
>
>
> --
>
> *Jaime Lopez Carvajal*
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>


-- 

*Jaime Lopez Carvajal*
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From imagepy at sina.com  Fri Dec  1 21:56:52 2017
From: imagepy at sina.com (imagepy at sina.com)
Date: Sat, 02 Dec 2017 10:56:52 +0800
Subject: [scikit-image] =?gbk?b?u9i4tKO6UmU6ICC72Li0o7pSZTogbXkgZmFzdCB3?=
 =?gbk?q?atershed_has_pass_all_the_test=5Fwatershed_check?=
Message-ID: <20171202025652.3202938054E@webmail.sinamail.sina.com.cn>

my code works for 2.7 and 3.x. I think it's matter of skimage's version. I remember the watershed_line parameter is added in version 13.0.
----- ???? -----
????Jaime Lopez Carvajal <jalopcar at gmail.com>
????imagepy at sina.com,  "Mailing list for scikit-image (http://scikit-image.org)" <scikit-image at python.org>
???Re: [scikit-image] ???Re: my fast watershed has pass all the test_watershed check
???2017?12?02? 10?48?

Hi YXDragon, 
Thanks for your test's description, I find them very clear.As I wrote to you, the problem only appear with tests that use the third parameter in skwatershed function, because your function works fine.
>out1 = watershed(data, markers, 2)     # works fine>out2 = skwatershed(data, markers, 2)  # does not work

I have installed skimage version 0.12.3 with python 2.7, maybe your code is for python 3.5?
Jaime


On Fri, Dec 1, 2017 at 8:47 PM,  <imagepy at sina.com> wrote:
Hi Jaime:All my test are in the following format:
def test_watershed01():    data = np.array(..., np.uint8)    markers = np.array(..., np.uint16)    out1 = mywatershed(data, markers)    out2 = skwatershed(data, markers)    print(np.sum(out1-out2!=0))
every test gets a zero output, but the parameter has little diffrence with skimage.1. the image should be uint8 (then region can growing one level in one step)2. the markers should be uint16 (I change -1 of the orignal test into 1, we just need to make sure the marker order)3. connectivity only accept 1 or 2. means 4-connect or 8 connect.(6-connect, 28-connect for 3d)
for the float image, I think we can do a histogram normalrize. this means take full use of the range.then scale into 0-255, if nessesary, scale into 0-65536, then my watershed can process it.
"Connectivity dimension must be same as image" I think it is generated by scikit-image, which version  do you use?
BestYXDragon----- ???? -----
????Jaime Lopez Carvajal <jalopcar at gmail.com>
????imagepy at sina.com,  "Mailing list for scikit-image (http://scikit-image.org)" <scikit-image at python.org>
???Re: [scikit-image] my fast watershed has pass all the test_watershed check
???2017?12?02? 05?47?

Hi YXDragon,
The majority of tests, except 1,3,9,11, generates this error: Connectivity dimension must be same as image
Do you think, I have an older version of skimage? or could it be another thing?
Jaime



On Wed, Nov 29, 2017 at 2:03 PM,  <imagepy at sina.com> wrote:
Hi Everyone:I had implemented a watershed by numba, and now it has pass all the test_watershed check and got a exactly same result with skimage, support watershed-line, support connectivity, (pass test 0-12, but mine did not support compact yet)
It support nd, now only support uint8 image with uint16 marks. (because I think sometimes it is enough, It can process float image if it is needed)
And it is very smart and fast. less than 100 lines, and faster than skimage one. a 3d image which skimage run more than 10 minutes ( and I cannot wait any longer, so kill it), but my watershed just need 28 s.
The code are attached. 
BestYXDragon
_______________________________________________

scikit-image mailing list

scikit-image at python.org

https://mail.python.org/mailman/listinfo/scikit-image




-- 
Jaime Lopez Carvajal




_______________________________________________

scikit-image mailing list

scikit-image at python.org

https://mail.python.org/mailman/listinfo/scikit-image




-- 
Jaime Lopez Carvajal



-------------- next part --------------
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From jalopcar at gmail.com  Fri Dec  1 22:27:33 2017
From: jalopcar at gmail.com (Jaime Lopez Carvajal)
Date: Fri, 1 Dec 2017 22:27:33 -0500
Subject: [scikit-image] =?utf-8?b?5Zue5aSN77yaUmU6IOWbnuWkje+8mlJlOiBt?=
	=?utf-8?q?y_fast_watershed_has_pass_all_the_test=5Fwatershed_check?=
In-Reply-To: <20171202025652.3202938054E@webmail.sinamail.sina.com.cn>
References: <20171202025652.3202938054E@webmail.sinamail.sina.com.cn>
Message-ID: <CANsMHoMe6qHnkNT-4PZwL-YHE5OTL3vrNQ7dF1M_x7YvMC541w@mail.gmail.com>

Hi YXdragon,

It works now, it was skimage version problem, I had 0.12.3.
I update it already to 0.13.1

Thank you very much, Jaime

On Fri, Dec 1, 2017 at 9:56 PM, <imagepy at sina.com> wrote:

> my code works for 2.7 and 3.x. I think it's matter of skimage's version. I
> remember the watershed_line parameter is added in version 13.0.
>
> ----- ???? -----
> ????Jaime Lopez Carvajal <jalopcar at gmail.com>
> ????imagepy at sina.com, "Mailing list for scikit-image (
> http://scikit-image.org)" <scikit-image at python.org>
> ???Re: [scikit-image] ???Re: my fast watershed has pass all the
> test_watershed check
> ???2017?12?02? 10?48?
>
> Hi YXDragon,
>
> Thanks for your test's description, I find them very clear.
> As I wrote to you, the problem only appear with tests that use the third
> parameter in *skwatershed function*, because your function works fine.
>
> >out1 = watershed(data, markers, *2*)     # works fine
> >out2 = skwatershed(data, markers, *2*)  # does not work
>
> I have installed skimage version 0.12.3 with python 2.7, maybe your code
> is for python 3.5?
>
> Jaime
>
>
>
> On Fri, Dec 1, 2017 at 8:47 PM, <imagepy at sina.com> wrote:
>
> Hi Jaime:
> All my test are in the following format:
>
> def test_watershed01():
>     data = np.array(..., np.uint8)
>     markers = np.array(..., np.uint16)
>     out1 = mywatershed(data, markers)
>     out2 = skwatershed(data, markers)
>     print(np.sum(out1-out2!=0))
>
> every test gets a zero output, but the parameter has little diffrence with
> skimage.
> 1. the image should be uint8 (then region can growing one level in one
> step)
> 2. the markers should be uint16 (I change -1 of the orignal test into 1,
> we just need to make sure the marker order)
> 3. connectivity only accept 1 or 2. means 4-connect or 8
> connect.(6-connect, 28-connect for 3d)
>
> for the float image, I think we can do a histogram normalrize. this means
> take full use of the range.
> then scale into 0-255, if nessesary, scale into 0-65536, then my watershed
> can process it.
>
> "Connectivity dimension must be same as image" I think it is generated by
> scikit-image, which version  do you use?
>
> Best
> YXDragon
> ----- ???? -----
> ????Jaime Lopez Carvajal <jalopcar at gmail.com>
> ????imagepy at sina.com, "Mailing list for scikit-image (
> http://scikit-image.org)" <scikit-image at python.org>
> ???Re: [scikit-image] my fast watershed has pass all the test_watershed
> check
> ???2017?12?02? 05?47?
>
> Hi YXDragon,
>
> The majority of tests, except 1,3,9,11, generates this error: Connectivity
> dimension must be same as image
>
> Do you think, I have an older version of skimage? or could it be another
> thing?
>
> Jaime
>
>
>
>
>
> On Wed, Nov 29, 2017 at 2:03 PM, <imagepy at sina.com> wrote:
>
> Hi Everyone:
> I had implemented a watershed by numba, and now it has pass all the
> test_watershed check and got a exactly same result with skimage, support
> watershed-line, support connectivity, (pass test 0-12, but mine did not
> support compact yet)
>
> It support nd, now only support uint8 image with uint16 marks. (because I
> think sometimes it is enough, It can process float image if it is needed)
>
> And it is very smart and fast. less than 100 lines, and faster than
> skimage one. a 3d image which skimage run more than 10 minutes ( and I
> cannot wait any longer, so kill it), but my watershed just need 28 s.
>
> The code are attached.
>
> Best
> YXDragon
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
>
>
> --
>
> *Jaime Lopez Carvajal*
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>
>
>
> --
>
> *Jaime Lopez Carvajal*
>
> _______________________________________________
> scikit-image mailing list
> scikit-image at python.org
> https://mail.python.org/mailman/listinfo/scikit-image
>
>


-- 

*Jaime Lopez Carvajal*
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