blob detection and dust removal

[Raphael]

hi Vighnesh,

  This is the error I got :

--------------------------------------------------------------------------TypeError                                 Traceback (most recent call last)<ipython-input-73-121959b15938> in <module>()      1 blobs_doh = blob_doh(img_equalized,  max_sigma=30, threshold=.1)----> 2 plt.imshow(blobs_doh)
/usr/lib/python3/dist-packages/matplotlib/pyplot.py in imshow(X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, hold, **kwargs)   2890                         vmax=vmax, origin=origin, extent=extent, shape=shape,   2891                         filternorm=filternorm, filterrad=filterrad,-> 2892                         imlim=imlim, resample=resample, url=url, **kwargs)   2893         draw_if_interactive()   2894     finally:
/usr/lib/python3/dist-packages/matplotlib/axes.py in imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, shape, filternorm, filterrad, imlim, resample, url, **kwargs)   7300                        filterrad=filterrad, resample=resample, **kwargs)   7301 -> 7302         im.set_data(X)   7303         im.set_alpha(alpha)   7304         self._set_artist_props(im)
/usr/lib/python3/dist-packages/matplotlib/image.py in set_data(self, A)    428         if (self._A.ndim not in (2, 3) or    429             (self._A.ndim == 3 and self._A.shape[-1] not in (3, 4))):--> 430             raise TypeError("Invalid dimensions for image data")    431     432         self._imcache = None
TypeError: Invalid dimensions for image data

I also printed blobs_doh and discovered it was an empty array..Don't know why it should be empty...

Thank you


On Sunday, 1 May 2016 01:48:13 UTC-7, Vighnesh Birodkar wrote:
>
> Hello Raphael
>
> What error did you get ? Can you post the traceback or the output after 
> blob detection ?
>
> Thanks
> Vighnesh
>
> On Saturday, April 30, 2016 at 2:02:51 AM UTC-4, Raphael wrote:
>>
>> hi folks,  
>>
>>   Got a problem removing dust and identifying blobs/crytals. Kindly see 
>> my code below
>>
>>
>> from __future__ import division, print_function
>> import matplotlib.pyplot as plt
>> import numpy as np
>> from skimage import io, feature, color, measure, draw, img_as_float, 
>> exposure
>> from skimage.filters.rank import median
>> from skimage.feature import blob_dog, blob_log, blob_doh
>> from skimage.morphology import disk
>>
>> #raw image
>> image_raw = 
>> img_as_float((io.imread('/home/raphael/Documents/ScikitImage/Run 
>> 4-2_00061cropped.tif'))) (RawImage.tif attached) 
>> plt.imshow(image_raw)
>>
>> #converted to grayscale
>>
>> img_gray = 
>> color.rgb2gray(io.imread('/home/raphael/Documents/ScikitImage/Run 
>> 4-2_00061cropped.tif'))
>> plt.imshow(image_gray)
>>
>>
>> #applied median filter to take out small dust particles. But the big dust 
>> particle on the top right corner still persists (see median1.png attached)
>> img_filtered=median(img_gray,disk(10))
>> plt.imshow(img_filtered)
>>
>>
>> #applied  adapthist to make image more clearer (see adaptive.png)
>>
>> img_equalized=exposure.equalize_adapthist(img_filtered)
>> plt.imshow(img_equalized)
>>
>> #trying to detect the crystals/blobs. I followed the example here 
>> http://scikit-image.org/docs/dev/auto_examples/features_detection/plot_blob.html 
>> But this gave an error. matplotlib was not happy with the data type
>> blobs_doh = blob_doh(img_equalized,  max_sigma=30, threshold=.1)
>> plt.imshow(blobs_doh) 
>>
>> My problems are:
>>
>> 1. I could not get the dust particle out especially the really big one on 
>> the top right. How can I get it out? 
>>
>> 2. I could not detect the crystals/blobs in the image using blob_doh
>>
>> Any ideas/suggestions is highly appreciated.  Thank you!
>>
>
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