How do I convert PALETTE COLOR pixel data to RGB?

[PankajSujyot]

I want following result

But I get following result

My code is as follows

plt.imsave(os.path.join(output_folder,str(i))+'.png', ds.pixel_array)  

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and with this change in code

plt.imsave(os.path.join(output_folder,str(i))+'.png', convert_color_space(ds.pixel_array, 'YBR_FULL', 'RGB'))  

I get following error

Could not convert:  operands could not be broadcast together with shapes (970,1616) (3,) (970,1616)

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DICOM File have following Details

I used

print(ds[0x00280000:0x00300000])
print(ds.file_meta.TransferSyntaxUID)

this line to print details

(0028, 0002) Samples per Pixel                   US: 1
(0028, 0004) Photometric Interpretation          CS: 'PALETTE COLOR'
(0028, 0010) Rows                                US: 970
(0028, 0011) Columns                             US: 1616
(0028, 0014) Ultrasound Color Data Present       US: 1
(0028, 0034) Pixel Aspect Ratio                  IS: [1, 1]
(0028, 0100) Bits Allocated                      US: 16
(0028, 0101) Bits Stored                         US: 16
(0028, 0102) High Bit                            US: 15
(0028, 0103) Pixel Representation                US: 0
(0028, 1101) Red Palette Color Lookup Table Desc US: [0, 0, 16]
(0028, 1102) Green Palette Color Lookup Table De US: [0, 0, 16]
(0028, 1103) Blue Palette Color Lookup Table Des US: [0, 0, 16]
(0028, 1201) Red Palette Color Lookup Table Data OW: Array of 131072 elements
(0028, 1202) Green Palette Color Lookup Table Da OW: Array of 131072 elements
(0028, 1203) Blue Palette Color Lookup Table Dat OW: Array of 131072 elements
(0028, 2110) Lossy Image Compression             CS: '00'
1.2.840.10008.1.2.5

---

1.txt
this is my row data file
please rename it ".txt" to ".raw" for use
.raw file is not supported here so I rename .raw file to .txt

I used following code to get .raw file

f = open(os.path.join(output_folder,str(i))+'.raw', "wb")
f.write(ds.pixel_array)                    
f.close()

[scaramallion]

You need to apply the palette colour LUT:

import matplotlib.pyplot as plt

from pydicom import dcmread
from pydicom.pixel_data_handlers.util import apply_color_lut

ds = dcmread(...)
arr = ds.pixel_array
rgb = apply_color_lut(arr, ds)
plt.imshow(rgb)
plt.show()

[PankajSujyot]

How to do it?

[scaramallion]

arr = numpy.clip((rgb / 2**8), 0, 255, dtype='uint8')

[PankajSujyot]

Could not convert: Cannot cast ufunc 'clip' input 0 from dtype('float64') to dtype('uint8') with casting rule 'same_kind'

[scaramallion]

arr = numpy.clip(rgb / 2**8, 0, 255, dtype='uint8', casting='unsafe')

[PankajSujyot]

thanks
I used following code

df_data = (rgb / (2**16 - 1))
inches = (10,6)
dpi = 150
fig, ax = plt.subplots(figsize=inches, dpi=dpi)
fig.subplots_adjust(left=0, right=1, top=1, bottom=0, wspace=0, hspace=0)
plt.imshow(df_data,vmin=-100, vmax=300)
plt.savefig(os.path.join(output_folder,file)+'.png')