How to set ImageItem colormaps in code

[Alex A]

Hello,
   I'm just starting with pyqtgraph, and somewhat new to Python overall, so apologies if this is something that is addressed somewhere else but I haven't been able to find it.   I'm trying to figure out how to set the colormap for an ImageItem in code rather than via the GradientEditor or other GUI methods. 
   For a trivial example, starting with the ImageItem.py example code I'd like to make it be just a gradient along the red intensity for values 0 to 0.5, then ramp the green from 0.5 to 1.0.  i.e.:
val -> R,G,B
0.0 -> 0,0,0
0.5 -> 255,0,0
1.0 -> 255,255,0

   It seems that the setLookupTable() is the function that should be used, but I can't seem to figure out exactly how to use it.   Could someone post what I'd need to add to the ImageItem.py example to accomplish this?

  Thanks

[Luke Campagnola]

Like this:

import numpy as np

import pyqtgraph as pg

# build lookup table

lut = np.zeros((256,3), dtype=np.ubyte)

lut[:128,0] = np.arange(0,255,2)

lut[128:,0] = 255

lut[:,1] = np.arange(255)

# random image data

img = np.random.normal(size=(100,100))

# GUI

win = pg.GraphicsWindow()

view = win.addViewBox()

view.setAspectLocked(True)

item = pg.ImageItem(img)

view.addItem(item)

item.setLookupTable(lut)

item.setLevels([0,1])

Equivalently, you could use a ColorMap to generate the lookup table:

pos = np.array([0.0, 0.5, 1.0])

color = np.array([[0,0,0,255], [255,128,0,255], [255,255,0,255]], dtype=np.ubyte)

map = pg.ColorMap(pos, color)

lut = map.getLookupTable(0.0, 1.0, 256)

Luke

[Alex A]

Luke,
   Thanks, that got me most of what I needed and I figured out some more on my own.   I case it's helpful for anyone else just starting out, below is what I modified the central part of the ImageItem.py example into for testing out the colormaps.  I realize it's a bit hacked, but it was just to test whether I understood some things.
   I was having some issues understanding how some of the parameters related to each other as well as when to call certain things.   In particular I was having a hard time at first figuring out why my color scale (i.e. the color of the background gradient in my example) kept changing as I added the solid bars before I realized I had to call setLevels() inside the updateData(). 

   Thanks again for the help,
          Alex


## Set initial view bounds
view.setRange(QtCore.QRectF(0, 0, 600, 600))

#create test pattern background, basically a gradient from left to right
gradCen=1000  #midpoint of gradient
data=np.zeros([15, 600, 600], dtype=np.uint16)
for i in range(data.shape[1]):
    data[:,i,:] = gradCen-(data.shape[1]/2)+i    
#add horizontal bars, the same color as the extremes of the gradient
data[5:10,:,200:210] = gradCen-300
data[5:10,:,300:310] = gradCen+300
#add horizontal bars, the color that should be the extremes of the colorscale
data[10:15,:,200:210] = 0
data[10:15,:,300:310] = gradCen*2


#create a color map that goes from full red, to yellow, then to full green
pos = np.array([0.0, 0.5, 1.0])  #absolute scale here relative to the expected data not important I believe
color = np.array([[255,0,0,255], [255,255,0,255], [0,255,0,255]], dtype=np.ubyte)
colmap = pg.ColorMap(pos, color)

#get LUT, first first two params should match the position scale extremes passed to ColorMap(). 
# I believe last one just has to be >= the difference between the min and max level set later
lut = colmap.getLookupTable(0, 1.0, 2000)

img.setLookupTable(lut)
#img.setLevels([0,2048])   #don't do here, it needs to be after each setImage to work properly


updateTime = ptime.time()
fps = 0
i = 0
def updateData():
    global img, data, i, updateTime, fps

    ## Display the data
    img.setImage(data[i])
    #set the levels to the min and max we desire on our scale
    img.setLevels([0,2000]) 
   
    i = (i+1) % data.shape[0]

    QtCore.QTimer.singleShot(200, updateData)
    now = ptime.time()
    fps2 = 1.0 / (now-updateTime)
    updateTime = now
    fps = fps * 0.9 + fps2 * 0.1
   
    #print "%0.1f fps" % fps

[Federico Barabas]

Is there a way to convert matplotlib colormaps to use them with pyqtgraph?

I'm specially interested in cubehelix:  matplotlib._cm.cubehelix

(https://www.mrao.cam.ac.uk/~dag/CUBEHELIX/)

[dyadkin]

Here it is:

#!/usr/bin/python
# -*- coding: utf-8 -*-

import numpy as np


# taken from https://www.mrao.cam.ac.uk/~dag/CUBEHELIX/cubehelix.py
lut_cubehelix = np.array((
    (0.00000, 0.00000, 0.00000),
    (2.04510, 0.34680, 1.68810),
    (4.02390, 0.71145, 3.45015),
    (5.93385, 1.10160, 5.28360),
    (7.76730, 1.51470, 7.18335),
    (9.52935, 1.95585, 9.14685),
    (11.20980, 2.42505, 11.16645),
    (12.80865, 2.92485, 13.23960),
    (14.32590, 3.46035, 15.36120),
    (15.75645, 4.02900, 17.52615),
    (17.10030, 4.63590, 19.73190),
    (18.35490, 5.27850, 21.97080),
    (19.52025, 5.96445, 24.23775),
    (20.59635, 6.68865, 26.53020),
    (21.57810, 7.45875, 28.84305),
    (22.47060, 8.26965, 31.16865),
    (23.26875, 9.12900, 33.50445),
    (23.97510, 10.03170, 35.84280),
    (24.59220, 10.98030, 38.18115),
    (25.11750, 11.97735, 40.51185),
    (25.55100, 13.02030, 42.83235),
    (25.89780, 14.11425, 45.13755),
    (26.15535, 15.25410, 47.41980),
    (26.32620, 16.44240, 49.67655),
    (26.41545, 17.67915, 51.90270),
    (26.42055, 18.96180, 54.09060),
    (26.34660, 20.29545, 56.24025),
    (26.19615, 21.67500, 58.34655),
    (25.96920, 23.10045, 60.40185),
    (25.67085, 24.57180, 62.40360),
    (25.30620, 26.08905, 64.34670),
    (24.87525, 27.65220, 66.22860),
    (24.38055, 29.25615, 68.04675),
    (23.82975, 30.90090, 69.79350),
    (23.22540, 32.58900, 71.46885),
    (22.57005, 34.31535, 73.07025),
    (21.86880, 36.07995, 74.59005),
    (21.12420, 37.88025, 76.02825),
    (20.34390, 39.71370, 77.38485),
    (19.53045, 41.58030, 78.65220),
    (18.68895, 43.47750, 79.83030),
    (17.82195, 45.40530, 80.91660),
    (16.93710, 47.35860, 81.91110),
    (16.03695, 49.33485, 82.81125),
    (15.12915, 51.33660, 83.61450),
    (14.21625, 53.35620, 84.32085),
    (13.30335, 55.39365, 84.93030),
    (12.39555, 57.44640, 85.44030),
    (11.50050, 59.51190, 85.85085),
    (10.61820, 61.58760, 86.16450),
    (9.75630, 63.67095, 86.37615),
    (8.92245, 65.75940, 86.49090),
    (8.11665, 67.85040, 86.50620),
    (7.34655, 69.94140, 86.42460),
    (6.61470, 72.03240, 86.24865),
    (5.92875, 74.11575, 85.97580),
    (5.29380, 76.19145, 85.60860),
    (4.70985, 78.25695, 85.15215),
    (4.18455, 80.31225, 84.60390),
    (3.72300, 82.34970, 83.96895),
    (3.32775, 84.36930, 83.24985),
    (3.00135, 86.36595, 82.44660),
    (2.75145, 88.34220, 81.56430),
    (2.58060, 90.29295, 80.60550),
    (2.49135, 92.21565, 79.57275),
    (2.48625, 94.10520, 78.46860),
    (2.57040, 95.96415, 77.30070),
    (2.74890, 97.78995, 76.06650),
    (3.01920, 99.57495, 74.77620),
    (3.38895, 101.32425, 73.42980),
    (3.85815, 103.03020, 72.03240),
    (4.43190, 104.69280, 70.58910),
    (5.10765, 106.30950, 69.10500),
    (5.89050, 107.88030, 67.58265),
    (6.78300, 109.40265, 66.02715),
    (7.78260, 110.87655, 64.44360),
    (8.89440, 112.29690, 62.83710),
    (10.11840, 113.66370, 61.21275),
    (11.45205, 114.97695, 59.57310),
    (12.90300, 116.23410, 57.92835),
    (14.46360, 117.43260, 56.27850),
    (16.13895, 118.57755, 54.63120),
    (17.92650, 119.66130, 52.99155),
    (19.82880, 120.68640, 51.36465),
    (21.84075, 121.65285, 49.75305),
    (23.96490, 122.55810, 48.16695),
    (26.19870, 123.40470, 46.60635),
    (28.54215, 124.18755, 45.07890),
    (30.99015, 124.91175, 43.58970),
    (33.54525, 125.57475, 42.14385),
    (36.20235, 126.17400, 40.74390),
    (38.96145, 126.71715, 39.39750),
    (41.81745, 127.19655, 38.10720),
    (44.76780, 127.61985, 36.88065),
    (47.81250, 127.98195, 35.72040),
    (50.94645, 128.28795, 34.62900),
    (54.16710, 128.53530, 33.61410),
    (57.46935, 128.72655, 32.67825),
    (60.85320, 128.86170, 31.82400),
    (64.30845, 128.94330, 31.05900),
    (67.83765, 128.97390, 30.38325),
    (71.43315, 128.95095, 29.80185),
    (75.09240, 128.87955, 29.31735),
    (78.80775, 128.76225, 28.93485),
    (82.57920, 128.59650, 28.65690),
    (86.39655, 128.38740, 28.48350),
    (90.25980, 128.13495, 28.42230),
    (94.16385, 127.84425, 28.46820),
    (98.10105, 127.51275, 28.63140),
    (102.06885, 127.14810, 28.90935),
    (106.05960, 126.74775, 29.30205),
    (110.07075, 126.31680, 29.81460),
    (114.09465, 125.85525, 30.44955),
    (118.12620, 125.37075, 31.20435),
    (122.16285, 124.85820, 32.07900),
    (126.19695, 124.32780, 33.07605),
    (130.22340, 123.77700, 34.19805),
    (134.23710, 123.21090, 35.44245),
    (138.23295, 122.62950, 36.80670),
    (142.20585, 122.04045, 38.29590),
    (146.15070, 121.44120, 39.90495),
    (150.06240, 120.83685, 41.63640),
    (153.93585, 120.22995, 43.48770),
    (157.76340, 119.62560, 45.45630),
    (161.54250, 119.02380, 47.53965),
    (165.27060, 118.42710, 49.74030),
    (168.93750, 117.84060, 52.05315),
    (172.54320, 117.26430, 54.47565),
    (176.08005, 116.70330, 57.00780),
    (179.54550, 116.15760, 59.64450),
    (182.93700, 115.63230, 62.38320),
    (186.24435, 115.12995, 65.22390),
    (189.47010, 114.65310, 68.15895),
    (192.60660, 114.20175, 71.18580),
    (195.65385, 113.78100, 74.30445),
    (198.60420, 113.39340, 77.50725),
    (201.45510, 113.04150, 80.79165),
    (204.20655, 112.72530, 84.15510),
    (206.85090, 112.44735, 87.58995),
    (209.39070, 112.21275, 91.09365),
    (211.82085, 112.02150, 94.66365),
    (214.13880, 111.87615, 98.29230),
    (216.34455, 111.77670, 101.97450),
    (218.43300, 111.72570, 105.70770),
    (220.40670, 111.72570, 109.48680),
    (222.26055, 111.77925, 113.30415),
    (223.99455, 111.88635, 117.15975),
    (225.60870, 112.04955, 121.04340),
    (227.10045, 112.26885, 124.95255),
    (228.47235, 112.54680, 128.87955),
    (229.72440, 112.88085, 132.82185),
    (230.85150, 113.27610, 136.77435),
    (231.86130, 113.73255, 140.72940),
    (232.74870, 114.24765, 144.68445),
    (233.51625, 114.82650, 148.63185),
    (234.16395, 115.46655, 152.56650),
    (234.69690, 116.17035, 156.48585),
    (235.11255, 116.93535, 160.38225),
    (235.41345, 117.76410, 164.25060),
    (235.60215, 118.65405, 168.08580),
    (235.68120, 119.60775, 171.88530),
    (235.65315, 120.62265, 175.64400),
    (235.51800, 121.69875, 179.35425),
    (235.28340, 122.83605, 183.01350),
    (234.94680, 124.03455, 186.61665),
    (234.51585, 125.29425, 190.16115),
    (233.99055, 126.61005, 193.63935),
    (233.37600, 127.98450, 197.05125),
    (232.67730, 129.41505, 200.38920),
    (231.89445, 130.90170, 203.65065),
    (231.03510, 132.44190, 206.83305),
    (230.10180, 134.03310, 209.93130),
    (229.09965, 135.67785, 212.94540),
    (228.03120, 137.37105, 215.86770),
    (226.90155, 139.11015, 218.70075),
    (225.71835, 140.89515, 221.43690),
    (224.48160, 142.72350, 224.07615),
    (223.20150, 144.59520, 226.61595),
    (221.87805, 146.50515, 229.05375),
    (220.51635, 148.45335, 231.38955),
    (219.12660, 150.43470, 233.61825),
    (217.70880, 152.45175, 235.74240),
    (216.26805, 154.49685, 237.76200),
    (214.81200, 156.57255, 239.66940),
    (213.34575, 158.67120, 241.47225),
    (211.87185, 160.79280, 243.16290),
    (210.39540, 162.93735, 244.74645),
    (208.92660, 165.09720, 246.22290),
    (207.46290, 167.27235, 247.58715),
    (206.01705, 169.46280, 248.84685),
    (204.58650, 171.66090, 249.99690),
    (203.18145, 173.86920, 251.04240),
    (201.80445, 176.08005, 251.98335),
    (200.46060, 178.29345, 252.82230),
    (199.15500, 180.50430, 253.55925),
    (197.89020, 182.71515, 254.19420),
    (196.67385, 184.91835, 254.73480),
    (195.50595, 187.11390, 255.00000),
    (194.39415, 189.29925, 255.00000),
    (193.34100, 191.47185, 255.00000),
    (192.34905, 193.62660, 255.00000),
    (191.42595, 195.76605, 255.00000),
    (190.56915, 197.88255, 255.00000),
    (189.78885, 199.97610, 255.00000),
    (189.08250, 202.04670, 255.00000),
    (188.45265, 204.08925, 255.00000),
    (187.90695, 206.10120, 255.00000),
    (187.44540, 208.08255, 255.00000),
    (187.06800, 210.03075, 254.69145),
    (186.77985, 211.94580, 254.25285),
    (186.58095, 213.82260, 253.76580),
    (186.47385, 215.66115, 253.23795),
    (186.46110, 217.45890, 252.66930),
    (186.54015, 219.21840, 252.06750),
    (186.71610, 220.93200, 251.43765),
    (186.98385, 222.60480, 250.78485),
    (187.35105, 224.22915, 250.11165),
    (187.81260, 225.81015, 249.42315),
    (188.36850, 227.34525, 248.72700),
    (189.02130, 228.83190, 248.02575),
    (189.76845, 230.27010, 247.32705),
    (190.60995, 231.65985, 246.63090),
    (191.54325, 233.00115, 245.94750),
    (192.57090, 234.29400, 245.27940),
    (193.68525, 235.53585, 244.63170),
    (194.88885, 236.72925, 244.00695),
    (196.17915, 237.87420, 243.41535),
    (197.55105, 238.97325, 242.85435),
    (199.00710, 240.02130, 242.33415),
    (200.53965, 241.02090, 241.85730),
    (202.14870, 241.97460, 241.42635),
    (203.82915, 242.88495, 241.04640),
    (205.57845, 243.74685, 240.72510),
    (207.39660, 244.56540, 240.45990),
    (209.27340, 245.34315, 240.26100),
    (211.20885, 246.07755, 240.12585),
    (213.20040, 246.77115, 240.06210),
    (215.24040, 247.42650, 240.06975),
    (217.32375, 248.04615, 240.15645),
    (219.45045, 248.63010, 240.31965),
    (221.61285, 249.18090, 240.56445),
    (223.80840, 249.70110, 240.89340),
    (226.02945, 250.19325, 241.30905),
    (228.27090, 250.65480, 241.81140),
    (230.53020, 251.09340, 242.40300),
    (232.80225, 251.51160, 243.08385),
    (235.07940, 251.90685, 243.85650),
    (237.35655, 252.28680, 244.72350),
    (239.63115, 252.64890, 245.68230),
    (241.89810, 253.00080, 246.73545),
    (244.14975, 253.34250, 247.88295),
    (246.37845, 253.67655, 249.12225),
    (248.58420, 254.00805, 250.45335),
    (250.76190, 254.33700, 251.87880),
    (252.90135, 254.66595, 253.39350),
    (255.00000, 255.00000, 255.00000)),
    dtype=np.ubyte
)

[Federico Barabas]

thanks a lot!

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[Federico Barabas]

For some reason it's not really working. Here's what I'm trying:

self.img = pg.ImageItem()

self.vb.addItem(self.img)

self.hist = pg.HistogramLUTItem()

self.hist.setImageItem(self.img)

self.img.setLookupTable(cubehelix())

where cubehelix is just a function that returns the lut_cubehelix array

what am I doing wrong?

[dyadkin]

I do not really know. I use ImageView widget and it works fine, I just had to subclass, otherwise if you resize the window, LUT drops to the default one. Now it works fine.

class ImageView(pg.ImageView):
    def __init__(self, *args, **kwargs):
        super(ImageView, self).__init__(*args, **kwargs)
        self.lut = None

    def updateImage(self, autoHistogramRange=True):
        super(ImageView, self).updateImage(autoHistogramRange)
        self.getImageItem().setLookupTable(self.lut)

    def setLookupTable(self, lut):
        self.lut = lut
        self.updateImage()

    def resizeEvent(self, event):
        super(ImageView, self).resizeEvent(event)
        self.updateImage()

Thus, just:

iv = ImageView()

iv.setLookupTable(cubehelix()) 

should work.

[dyadkin]

Finally, I have written a generator of lookup table for pyqtgraph.

Cubehelix:

def cubehelix(gamma=1.0, s=0.5, r=-1.5, h=1.0):
    def get_color_function(p0, p1):
        def color(x):
            xg = x ** gamma
            a = h * xg * (1 - xg) / 2
            phi = 2 * np.pi * (s / 3 + r * x)
            return xg + a * (p0 * np.cos(phi) + p1 * np.sin(phi))
        return color

    array = np.empty((256, 3))
    abytes = np.arange(0, 1, 1/256.)
    array[:, 0] = get_color_function(-0.14861, 1.78277)(abytes) * 255
    array[:, 1] = get_color_function(-0.29227, -0.90649)(abytes) * 255
    array[:, 2] = get_color_function(1.97294, 0.0)(abytes) * 255
    return array

Rainbow:

def rainbow():
    array = np.empty((256, 3))
    abytes = np.arange(0, 1, 0.00390625)
    array[:, 0] = np.abs(2 * abytes - 0.5) * 255
    array[:, 1] = np.sin(abytes * np.pi) * 255
    array[:, 2] = np.cos(abytes * np.pi / 2) * 255
    return array

[Federico Barabas]

Awesome!

I didn't want to use an ImageView, so in the update routine I did this:

self.img.setImage(image, autoLevels=False, lut=self.lut)

where self.lut points to the cubehelix

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[Federico Barabas]

The only (small) thing that bugs me is the fact that the gradient in the HistogramLutItem doesn't reflect the cubehelix gradient

[Luke Campagnola]

If you are using ImageView, then you can assign a colormap to the gradient editor rather than the image:

    imageview.ui.histogram.gradient.setColorMap(colormap)

This should also make it unnecessary to deal with the widget resize resetting the LUT. 

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[Federico Barabas]

ok, but I think that's not so easy because the cubehelix lut has a continous change in color, so I can't think of a way of creating a colormap with positions

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[Federico Barabas]

I went over this thing again and I managed to change the gradient to the cubehelix colormap in this way:

I got the cubehelix RGB array from https://www.mrao.cam.ac.uk/~dag/CUBEHELIX/cubehelix.py. And then these lines made the trick:

        hist = pyqtgraph.HistogramLUTItem()

        cubehelix = cubehelix().astype(int)

        pos, color = np.arange(0, 1, 1/256), cubehelix

        hist.gradient.setColorMap(pyqtgraph.ColorMap(pos, color))

One question remains: is there an easy way of hiding all the ticks next to the gradient? I don't need them and they don't look good because the colormap has a tick for each position between 0 and 255. I tried subclassing TickSliderItem but in the end I failed.

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[Luke Campagnola]

I would love it if we could move away from using lookup tables and toward a more general colormapping model. The ColorMap class was intended to be a start in this direction, but I think this would take a lot more work to sort out.

On Mon, Jul 11, 2016 at 4:23 PM, Federico Barabas <fede.b...@gmail.com> wrote:

One question remains: is there an easy way of hiding all the ticks next to the gradient? I don't need them and they don't look good because the colormap has a tick for each position between 0 and 255. I tried subclassing TickSliderItem but in the end I failed.

I suppose the easiest way is just to hide the ticks after you set the gradient, and maybe adjust the width of the gradient editor, like:

  for tick in histogramLutItem.gradient.ticks:

      tick.hide()

  histogramLutItem.gradient.setFixedWidth(...)

[Federico Barabas]

Thank you Luke! I'm sorry I missed that simple hide command

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