Problem coloring symbols in pygmt v0.11 with plot and plot3d commands

[WilliamEpenarandaA]

Description of the problem

Greetings,

I'm having troubles filling symbols with the colors based on a different variable using PyGMT v0.11 and GMT 6.3 plot3d commands in Ubuntu 18.04 OS. This is the same issue reported in this post https://forum.generic-mapping-tools.org/t/coloring-symbols-with-cpt-pygmt/4034. I have seen other comments, but none of them seem to work for my case.

I test the example 3d scatter plot found in the pygmt webpage and works normally. The problem appeared when I try to plot in 3d view some earthquakes and colored according to different depth values. The data is saved into a pandas dataframe, data_dev that have this structure:

Index	Date	Hour_UTC	Latitude	Longitude	SGC_depth	Mw_x	Lat-cent	Lon-cent	Mt_depth	Mw_y	Pdc	Pclvd	Piso	Variance	VarRed
0	2015-09-07	17:35:31	6.815	-73.145	150.10	4.4	6.815	-73.055	135	6.03	85	15	0	6.866000e-08	54.48
1	2013-12-30	00:12:58	6.811	-73.146	152.00	4.5	6.947	-73.146	155	4.54	96	4	0	3.432000e-11	56.96
2	2018-01-21	17:51:59	6.837	-73.139	147.70	4.6	6.656	-72.958	195	5.35	59	41	0	1.373000e-08	42.88
3	2014-03-30	08:36:59	6.796	-73.155	142.20	4.6	6.977	-73.336	160	4.96	56	44	0	1.724000e-10	72.48
4	2014-11-20	05:40:10	6.817	-73.165	153.60	4.7	6.998	-73.029	135	4.51	61	39	0	1.382000e-11	88.70
5	2016-02-11	07:14:37	6.818	-73.135	154.20	4.7	6.637	-72.999	146	4.49	56	44	0	3.606000e-11	62.59
6	2017-02-01	00:18:26	6.773	-73.164	149.00	4.7	6.773	-73.345	115	4.31	84	16	0	1.469000e-11	67.57
7	2018-02-04	15:11:17	6.823	-73.159	152.60	4.7	6.642	-72.978	125	5.38	68	32	0	7.063000e-09	72.24
8	2016-06-23	22:28:56	6.815	-73.162	149.10	4.7	6.679	-72.981	135	5.81	63	37	0	2.076000e-08	48.97

Below is the code than I'm using

#%% Import the require modulus
import pandas as pd
import pygmt
import matplotlib.pyplot as plt
import os

## Loading the data needed
file = 'MT-dev_inv-results.xlsx'
basepath = os.path.split(os.path.dirname(__file__))[0]
filepath = os.path.join(basepath, file)
cols2_use = ['Date', 'Hour_UTC', 'Latitude', 'Longitude', 'SGC_depth', 'Lat-cent', 'Lon-cent', 'Mt_depth', 'Variance',\
    'VarRed', 'Pdc', 'Pclvd', 'Piso', 'Mw_x', 'Mw_y']

data_dev = pd.read_excel(filepath, usecols=cols2_use)

#%% Drawing the 3d perspective view
region=pygmt.info(data=data_dev[['Longitude', 'Latitude', 'SGC_depth']], 
    per_column=True, spacing=(0.2, 0.2, 50))

fig = pygmt.Figure()

pygmt.makecpt(cmap="viridis", 
              series=(100, 200, 1), 
              reverse=None, 
              continuous=None,
)
fig.plot3d(x=data_dev['Longitude'], y=data_dev['Latitude'], z=data_dev['SGC_depth'],\
cmap=True, style='u0.15c', region=region, size=data_dev['Mw_x']*1.2,
perspective=[240, 30], zscale=-0.05
)
fig.plot3d(x=data_dev['Lon-cent'], y=data_dev['Lat-cent'], z=data_dev['Mt_depth'],\
cmap=True, style='u0.3c', region=region, size=data_dev['Mw_y']*1.2, \
perspective=[240, 30], zscale=-0.05, frame=["WSneZ", "xa0.2f0.1g0.1+lLongitude [°]", "ya0.2f0.1g0.1+lLatitude [°]", "za50f20g20+lDepth [km]"]
)
fig.colorbar(frame=["a20f10", "y+lkm"], position="JRM")
fig.show()

The figure that it creates is the following and in the console doesn't appear any error or warning The code runs, but all the cubes plot black instead of using the color palette that I assigned in makecpt. Is there any problem or error in the code wrote to plot the image.

Thank in advance for your help!!!

PD: I attach the output to the command pygmt.show_versions() below:

PyGMT information: version: v0.11.0 System information: python: 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0] executable: /home/william/anaconda3/envs/pygmt/bin/python machine: Linux-5.4.0-150-generic-x86_64-with-glibc2.27 Dependency information: numpy: 1.26.4 pandas: 2.2.2 xarray: 2024.3.0 netCDF4: 1.6.5 packaging: 24.0 contextily: None geopandas: None ipython: None rioxarray: None ghostscript: 10.03.0 GMT library information: binary version: 6.5.0 cores: 12 grid layout: rows image layout: library path: /home/william/anaconda3/envs/pygmt/lib/libgmt.so padding: 2 plugin dir: /home/william/anaconda3/envs/pygmt/lib/gmt/plugins share dir: /home/william/anaconda3/envs/pygmt/share/gmt version: 6.5.0

Minimal Complete Verifiable Example

No response

Full error message

No response

System information

PyGMT information:
  version: v0.11.0
System information:
  python: 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
  executable: /home/william/anaconda3/envs/pygmt/bin/python
  machine: Linux-5.4.0-150-generic-x86_64-with-glibc2.27
Dependency information:
  numpy: 1.26.4
  pandas: 2.2.2
  xarray: 2024.3.0
  netCDF4: 1.6.5
  packaging: 24.0
  contextily: None
  geopandas: None
  ipython: None
  rioxarray: None
  ghostscript: 10.03.0
GMT library information:
  binary version: 6.5.0
  cores: 12
  grid layout: rows
  image layout: 
  library path: /home/william/anaconda3/envs/pygmt/lib/libgmt.so
  padding: 2
  plugin dir: /home/william/anaconda3/envs/pygmt/lib/gmt/plugins
  share dir: /home/william/anaconda3/envs/pygmt/share/gmt
  version: 6.5.0

[welcome[bot]]

👋 Thanks for opening your first issue here! Please make sure you filled out the template with as much detail as possible. You might also want to take a look at our contributing guidelines and code of conduct.

[seisman]

Perhaps you need to set the fill like fill=data_dev['SGC_depth'].

[yvonnefroehlich]

I think there are two options to accomplish color-coding (and size-coding) (see the code example below):

• Use x, y, z, fill(, and size) parameters (see also the comment by @seisman)
• Use the data parameter (column order must be x/lon, y/lat, z/depth, quantity_for_color, quantity_for_size)

Another aspect is that you set the size parameter, but before you have already set a fixed size via the style parameter.

Input data: MT-dev_inv-results.txt

import pandas as pd
import pygmt

file = "MT-dev_inv-results.txt"
cols2_use = [
    "Date", "Hour_UTC", "Latitude", "Longitude", "SGC_depth",
    "Lat-cent", "Lon-cent", "Mt_depth", "Variance",
    "VarRed", "Pdc", "Pclvd", "Piso", "Mw_x", "Mw_y",
]
data_dev = pd.read_csv(file, usecols=cols2_use, delimiter=" ")

region = pygmt.info(
    data=data_dev[["Longitude", "Latitude", "SGC_depth"]],
    per_column=True,
    spacing=(0.2, 0.2, 50),
)

fig = pygmt.Figure()

pygmt.makecpt(cmap="viridis", series=(100, 200, 1), continuous=None)

fig.plot3d(
    x=data_dev["Longitude"],
    y=data_dev["Latitude"],
    z=data_dev["SGC_depth"],
    fill=data_dev["SGC_depth"],
# OR
    # data=data_dev[["Longitude", "Latitude", "SGC_depth", "SGC_depth"]],
    cmap=True,
    style="u0.15c",
    region=region,
    # size=data_dev["Mw_x"]*1.2,  # Ignored when a fixed size via style is set
    perspective=[240, 30],
    zscale=-0.05,
)
fig.plot3d(
    # x=data_dev["Lon-cent"],
    # y=data_dev["Lat-cent"],
    # z=data_dev["Mt_depth"],
    # fill=data_dev["Mt_depth"],
# OR
    data=data_dev[["Lon-cent", "Lat-cent", "Mt_depth", "Mt_depth"]],
    cmap=True,
    style="u0.3c",
    region=region,
    perspective=[240, 30],
    zscale=-0.05,
    frame=[
        "WSneZ",
        "xa0.2f0.1g0.1+lLongitude [°]",
        "ya0.2f0.1g0.1+lLatitude [°]",
        "za50f20g20+lDepth [km]",
    ]
)

fig.colorbar(frame=["a20f10", "y+lkm"], position="JRM")

fig.show()

[WilliamEpenarandaA]

Thanks for your comments. Including the line proposed by @seisman, solve the problem. I see that the input in fill parameter, need to put values of the variable used to make the correspond colorbar. I also thanks the explannation given to generate size-coding by @yvonnefroehlich