I've been creating graphs with the networkx package and everything works fine. I would like to make the graphs even better by placing the bigger nodes in the middle of the graph and the layout functions from networkx does not seem to do the job. The nodes represent the size of degree (the higher connected the node, the bigger).
Is there any way to program these graphs in such a way that the bigger nodes are positioned in the middle? It does not have to be automated, i could also manually choose the nodes and give them the middle position but i can also not find how to do this.
If this is not possible with networkx or something else; is there any way to do it with Gephi or cytoscape? I had trouble with Gephi that it does not import the graph the same way i see it in my jupyter notebook (the colors, the node- and edge-sizes do not import).
To summarize; i want to put bigger nodes in the middle of my graph but i dont mind how i get it done (with networkx, matplotlib or whatever).
Unfortunately i cannot provide my actual graphs but here is an example which can look like one of my graphs; it is a directed weighted graph.
G = nx.gnp_random_graph(15, 0.2, directed=True)
d = dict(G.degree(weight='weight'))
d = {k: v/10 for k, v in d.items()}
edge_size = [(float(i)/sum(weights))*100 for i in weights]
node_size = [(v*1000) for v in d.values()]
nx.draw(G,width=edge_size,node_size=node_size)
There are several options:
import networkx as nx
G = nx.gnp_random_graph(15, 0.2, directed=True)
node_degree = dict(G.degree(weight='weight'))
# A) Precompute node positions, and then manually over-ride some node positions.
node_positions = nx.spring_layout(G)
node_positions[0] = (0.5, 0.5) # by default, networkx plots on a canvas with the origin at (0, 0) and a width and height of 1; (0.5, 0.5) is hence the center
nx.draw(G, pos=node_positions, node_size=[100 * node_degree[node] for node in G])
plt.show()
# B) Use netgraph to draw the graph and then drag the nodes around with the mouse.
from netgraph import InteractiveGraph # pip install netgraph
plot_instance = InteractiveGraph(G, node_size=node_degree)
plt.show()
# C) Modify the Fruchterman-Reingold algorithm to include a gravitational force that pulls nodes with a large "mass" towards the center.
# This is left as an exercise to the interested reader (i.e. very non-trivial).
Edit: option C is non-trivial but also very do-able.
Here is my stab at it.
#!/usr/bin/env python
# coding: utf-8
"""
FR layout but with an additional gravitational pull towards a gravitational center.
The pull is proportional to the mass of the node.
"""
import numpy as np
import matplotlib.pyplot as plt
# pip install netgraph
from netgraph._main import BASE_SCALE
from netgraph._utils import (
_get_unique_nodes,
_edge_list_to_adjacency_matrix,
)
from netgraph._node_layout import (
_is_within_bbox,
_get_temperature_decay,
_get_fr_repulsion,
_get_fr_attraction,
_rescale_to_frame,
_handle_multiple_components,
_reduce_node_overlap,
)
DEBUG = False
#_handle_multiple_components
def get_fruchterman_reingold_newton_layout(edges,
edge_weights = None,
k = None,
g = 1.,
scale = None,
origin = None,
gravitational_center = None,
initial_temperature = 1.,
total_iterations = 50,
node_size = 0,
node_mass = 1,
node_positions = None,
fixed_nodes = None,
*args, **kwargs):
"""Modified Fruchterman-Reingold node layout.
Uses a modified Fruchterman-Reingold algorithm [Fruchterman1991]_ to compute node positions.
This algorithm simulates the graph as a physical system, in which nodes repell each other.
For connected nodes, this repulsion is counteracted by an attractive force exerted by the edges, which are simulated as springs.
Unlike the original algorithm, there is an additional attractive force pulling nodes towards a gravitational center, in proportion to their masses.
Parameters
----------
edges : list
The edges of the graph, with each edge being represented by a (source node ID, target node ID) tuple.
edge_weights : dict
Mapping of edges to edge weights.
k : float or None, default None
Expected mean edge length. If None, initialized to the sqrt(area / total nodes).
g : float or None, default 1.
Gravitational constant that sets the magnitude of the gravitational pull towards the center.
origin : tuple or None, default None
The (float x, float y) coordinates corresponding to the lower left hand corner of the bounding box specifying the extent of the canvas.
If None is given, the origin is placed at (0, 0).
scale : tuple or None, default None
The (float x, float y) dimensions representing the width and height of the bounding box specifying the extent of the canvas.
If None is given, the scale is set to (1, 1).
gravitational_center : tuple or None, default None
The (float x, float y) coordinates towards which nodes experience a gravitational pull.
If None, the gravitational center is placed at the center of the canvas defined by origin and scale.
total_iterations : int, default 50
Number of iterations.
initial_temperature: float, default 1.
Temperature controls the maximum node displacement on each iteration.
Temperature is decreased on each iteration to eventually force the algorithm into a particular solution.
The size of the initial temperature determines how quickly that happens.
Values should be much smaller than the values of `scale`.
node_size : scalar or dict, default 0.
Size (radius) of nodes.
Providing the correct node size minimises the overlap of nodes in the graph,
which can otherwise occur if there are many nodes, or if the nodes differ considerably in size.
node_mass : scalar or dict, default 1.
Mass of nodes.
Nodes with higher mass experience a larger gravitational pull towards the center.
node_positions : dict or None, default None
Mapping of nodes to their (initial) x,y positions. If None are given,
nodes are initially placed randomly within the bounding box defined by `origin` and `scale`.
If the graph has multiple components, explicit initial positions may result in a ValueError,
if the initial positions fall outside of the area allocated to that specific component.
fixed_nodes : list or None, default None
Nodes to keep fixed at their initial positions.
Returns
-------
node_positions : dict
Dictionary mapping each node ID to (float x, float y) tuple, the node position.
References
----------
.. [Fruchterman1991] Fruchterman, TMJ and Reingold, EM (1991) ‘Graph drawing by force‐directed placement’,
Software: Practice and Experience
"""
# This is just a wrapper around `_fruchterman_reingold`, which implements (the loop body of) the algorithm proper.
# This wrapper handles the initialization of variables to their defaults (if not explicitely provided),
# and checks inputs for self-consistency.
assert len(edges) > 0, "The list of edges has to be non-empty."
if origin is None:
if node_positions:
minima = np.min(list(node_positions.values()), axis=0)
origin = np.min(np.stack([minima, np.zeros_like(minima)], axis=0), axis=0)
else:
origin = np.zeros((2))
else:
# ensure that it is an array
origin = np.array(origin)
if scale is None:
if node_positions:
delta = np.array(list(node_positions.values())) - origin[np.newaxis, :]
maxima = np.max(delta, axis=0)
scale = np.max(np.stack([maxima, np.ones_like(maxima)], axis=0), axis=0)
else:
scale = np.ones((2))
else:
# ensure that it is an array
scale = np.array(scale)
assert len(origin) == len(scale), \
"Arguments `origin` (d={}) and `scale` (d={}) need to have the same number of dimensions!".format(len(origin), len(scale))
dimensionality = len(origin)
if gravitational_center is None:
gravitational_center = origin + 0.5 * scale
else:
# ensure that it is an array
gravitational_center = np.array(gravitational_center)
if fixed_nodes is None:
fixed_nodes = []
connected_nodes = _get_unique_nodes(edges)
if node_positions is None: # assign random starting positions to all nodes
node_positions_as_array = np.random.rand(len(connected_nodes), dimensionality) * scale + origin
unique_nodes = connected_nodes
else:
# 1) check input dimensionality
dimensionality_node_positions = np.array(list(node_positions.values())).shape[1]
assert dimensionality_node_positions == dimensionality, \
"The dimensionality of values of `node_positions` (d={}) must match the dimensionality of `origin`/ `scale` (d={})!".format(dimensionality_node_positions, dimensionality)
is_valid = _is_within_bbox(list(node_positions.values()), origin=origin, scale=scale)
if not np.all(is_valid):
error_message = "Some given node positions are not within the data range specified by `origin` and `scale`!"
error_message += "\n\tOrigin : {}, {}".format(*origin)
error_message += "\n\tScale : {}, {}".format(*scale)
error_message += "\nThe following nodes do not fall within this range:"
for ii, (node, position) in enumerate(node_positions.items()):
if not is_valid[ii]:
error_message += "\n\t{} : {}".format(node, position)
error_message += "\nThis error can occur if the graph contains multiple components but some or all node positions are initialised explicitly (i.e. node_positions != None)."
raise ValueError(error_message)
# 2) handle discrepancies in nodes listed in node_positions and nodes extracted from edges
if set(node_positions.keys()) == set(connected_nodes):
# all starting positions are given;
# no superfluous nodes in node_positions;
# nothing left to do
unique_nodes = connected_nodes
else:
# some node positions are provided, but not all
for node in connected_nodes:
if not (node in node_positions):
warnings.warn("Position of node {} not provided. Initializing to random position within frame.".format(node))
node_positions[node] = np.random.rand(2) * scale + origin
unconnected_nodes = []
for node in node_positions:
if not (node in connected_nodes):
unconnected_nodes.append(node)
fixed_nodes.append(node)
# warnings.warn("Node {} appears to be unconnected. The current node position will be kept.".format(node))
unique_nodes = connected_nodes + unconnected_nodes
node_positions_as_array = np.array([node_positions[node] for node in unique_nodes])
total_nodes = len(unique_nodes)
if isinstance(node_size, (int, float)):
node_size = node_size * np.ones((total_nodes))
elif isinstance(node_size, dict):
node_size = np.array([node_size[node] if node in node_size else 0. for node in unique_nodes])
if isinstance(node_mass, (int, float)):
node_mass = node_mass * np.ones((total_nodes))
elif isinstance(node_mass, dict):
node_mass = np.array([node_mass[node] if node in node_mass else 0. for node in unique_nodes])
adjacency = _edge_list_to_adjacency_matrix(
edges, edge_weights=edge_weights, unique_nodes=unique_nodes)
# Forces in FR are symmetric.
# Hence we need to ensure that the adjacency matrix is also symmetric.
adjacency = adjacency + adjacency.transpose()
if fixed_nodes:
is_mobile = np.array([False if node in fixed_nodes else True for node in unique_nodes], dtype=bool)
mobile_positions = node_positions_as_array[is_mobile]
fixed_positions = node_positions_as_array[~is_mobile]
mobile_node_sizes = node_size[is_mobile]
fixed_node_sizes = node_size[~is_mobile]
mobile_node_masses = node_mass[is_mobile]
fixed_node_masses = node_mass[~is_mobile]
# reorder adjacency
total_mobile = np.sum(is_mobile)
reordered = np.zeros((adjacency.shape[0], total_mobile))
reordered[:total_mobile, :total_mobile] = adjacency[is_mobile][:, is_mobile]
reordered[total_mobile:, :total_mobile] = adjacency[~is_mobile][:, is_mobile]
adjacency = reordered
else:
is_mobile = np.ones((total_nodes), dtype=bool)
mobile_positions = node_positions_as_array
fixed_positions = np.zeros((0, 2))
mobile_node_sizes = node_size
fixed_node_sizes = np.array([])
mobile_node_masses = node_mass
fixed_node_masses = np.array([])
if k is None:
area = np.product(scale)
k = np.sqrt(area / float(total_nodes))
temperatures = _get_temperature_decay(initial_temperature, total_iterations)
# --------------------------------------------------------------------------------
# main loop
for ii, temperature in enumerate(temperatures):
candidate_positions = _fruchterman_reingold_newton(mobile_positions, fixed_positions,
mobile_node_sizes, fixed_node_sizes,
adjacency, temperature, k,
mobile_node_masses, fixed_node_masses,
gravitational_center, g)
is_valid = _is_within_bbox(candidate_positions, origin=origin, scale=scale)
mobile_positions[is_valid] = candidate_positions[is_valid]
# --------------------------------------------------------------------------------
# format output
node_positions_as_array[is_mobile] = mobile_positions
if np.all(is_mobile):
node_positions_as_array = _rescale_to_frame(node_positions_as_array, origin, scale)
node_positions = dict(zip(unique_nodes, node_positions_as_array))
return node_positions
def _fruchterman_reingold_newton(mobile_positions, fixed_positions,
mobile_node_radii, fixed_node_radii,
adjacency, temperature, k,
mobile_node_masses, fixed_node_masses,
gravitational_center, g):
"""Inner loop of modified Fruchterman-Reingold layout algorithm."""
combined_positions = np.concatenate([mobile_positions, fixed_positions], axis=0)
combined_node_radii = np.concatenate([mobile_node_radii, fixed_node_radii])
delta = mobile_positions[np.newaxis, :, :] - combined_positions[:, np.newaxis, :]
distance = np.linalg.norm(delta, axis=-1)
# alternatively: (hack adapted from igraph)
if np.sum(distance==0) - np.trace(distance==0) > 0: # i.e. if off-diagonal entries in distance are zero
warnings.warn("Some nodes have the same position; repulsion between the nodes is undefined.")
rand_delta = np.random.rand(*delta.shape) * 1e-9
is_zero = distance <= 0
delta[is_zero] = rand_delta[is_zero]
distance = np.linalg.norm(delta, axis=-1)
# subtract node radii from distances to prevent nodes from overlapping
distance -= mobile_node_radii[np.newaxis, :] + combined_node_radii[:, np.newaxis]
# prevent distances from becoming less than zero due to overlap of nodes
distance[distance <= 0.] = 1e-6 # 1e-13 is numerical accuracy, and we will be taking the square shortly
with np.errstate(divide='ignore', invalid='ignore'):
direction = delta / distance[..., None] # i.e. the unit vector
# calculate forces
repulsion = _get_fr_repulsion(distance, direction, k)
attraction = _get_fr_attraction(distance, direction, adjacency, k)
gravity = _get_gravitational_pull(mobile_positions, mobile_node_masses, gravitational_center, g)
if DEBUG:
r = np.median(np.linalg.norm(repulsion, axis=-1))
a = np.median(np.linalg.norm(attraction, axis=-1))
g = np.median(np.linalg.norm(gravity, axis=-1))
print(r, a, g)
displacement = attraction + repulsion + gravity
# limit maximum displacement using temperature
displacement_length = np.linalg.norm(displacement, axis=-1)
displacement = displacement / displacement_length[:, None] * np.clip(displacement_length, None, temperature)[:, None]
mobile_positions = mobile_positions + displacement
return mobile_positions
def _get_gravitational_pull(mobile_positions, mobile_node_masses, gravitational_center, g):
delta = gravitational_center[np.newaxis, :] - mobile_positions
direction = delta / np.linalg.norm(delta, axis=-1)[:, np.newaxis]
magnitude = mobile_node_masses - np.mean(mobile_node_masses)
return g * magnitude[:, np.newaxis] * direction
if __name__ == '__main__':
import networkx as nx
from netgraph import Graph
G = nx.gnp_random_graph(15, 0.2, directed=True)
node_degree = dict(G.degree(weight='weight'))
node_positions = get_fruchterman_reingold_newton_layout(
list(G.edges()),
node_size={node : BASE_SCALE * degree for node, degree in node_degree.items()},
node_mass=node_degree, g=2
)
Graph(G, node_layout=node_positions, node_size=node_degree)
plt.show()
I am trying to use ESRI latest land use data and downloaded a tif image from
https://www.arcgis.com/apps/instant/media/index.html?appid=fc92d38533d440078f17678ebc20e8e2
for example, shown here
https://lulctimeseries.blob.core.windows.net/lulctimeseriespublic/lc2021/16R_20210101-20220101.tif
When I load the image to ArcGIS pro, the longitude between A and B (corners) is 6 degrees, which is expected. The tif image is in WGS84/UTM 16N projection. I want to be able to find longitude and latitude of each pixels on the tif file, so I converted it to WGS 84 coordinate. However, after I converted it (by GDAL and ArcGIS), the longitude span between A and B is larger than 6 degrees. It looks like the transformer treat each grid on the image as equal distance instead of equal longitude/latitude. Am I doing something wrong here?
def wgs_transformer(img):
"""Giving geoio image, return two transformers from image crs to wgs84 and wgs84 to image crs
They can be used to translate between pixels and lat/long
"""
assert isinstance(img, geoio.base.GeoImage), 'img is not geoio.base.GeoImage type object'
old_cs= osr.SpatialReference()
old_cs.ImportFromWkt(img.ds.GetProjectionRef())
# create the new coordinate system
new_cs = osr.SpatialReference()
new_cs.ImportFromEPSG(4326)
# create a transform object to convert between coordinate systems
transform_img_wgs = osr.CoordinateTransformation(old_cs,new_cs)
transform_wgs_img = osr.CoordinateTransformation(new_cs, old_cs)
return transform_img_wgs, transform_wgs_img
def pixels_to_latlong(img, px, py, transform, arr=None, return_band=False):
"""Giving pixels x, y cordinates, return latitude and longitude
Args:
img: geoio.base.GeoImage
px: float, x cordinate
py: float, y cordinate
transfrom: osgeo.osr.CoordinateTransformation
arr: np array, band info of the img
return_band: bool, if Ture, return band info for the pixel
Returns:
latitude, longitude
"""
assert isinstance(img, geoio.base.GeoImage), 'img is not geoio.base.GeoImage type object'
assert isinstance(transform, osgeo.osr.CoordinateTransformation), 'transform has to be osgeo.osr.CoordinateTransformation object'
band, width, height = img.shape
assert 0 <= px < width and 0 <= py < height, f'px {px}, py {py} are beyond the img shape ({width}, {height})'
if return_band:
assert isinstance(arr, np.ndarray), 'arr needs to be numpy.ndarray'
lat, long, _ = transform.TransformPoint(*img.raster_to_proj(px, py))
if return_band:
band_val = arr[py-1, px-1]
return lat, long, band_val
else:
return lat, long, 0
Using the Haversine formula for distance calculation on a great circle, I use the following code to calculate the coordinates of any point between a known start location (with lat1/lon1) and a known destination (with lat2/lon2):
Here's the complete code:
from math import radians, sin, cos, acos, atan2, sqrt, pi
#enter the following numbers in the corresponding input fields:
#lat1 = starting latitude = 33.95
#lon1 = starting longitude = -118.40
#lat2 = destination latitude = 40.6333
#lon2= destination longitude = -73.7833
lat1 = radians(float(input("Starting latitude: ")))
lon1 = radians(float(input("Starting longitude: ")))
lat2 = radians(float(input("Destination latitude: ")))
lon2 = radians(float(input("Destination longitude: ")))
#Haversine formula to calculate the distance, in radians, between starting point and destination:
d = ((6371.01 * acos(sin(lat1)*sin(lat2) + cos(lat1)*cos(lat2)*cos(lon1 - lon2)))/1.852)/(180*60/pi)
import numpy as np
x = np.arange(0, 1, 0.2)
for f in x:
A=sin((1-f)*d)/sin(d)
B=sin(f*d)/sin(d)
x = A*cos(lat1)*cos(lon1) + B*cos(lat2)*cos(lon2)
y = A*cos(lat1)*sin(lon1) + B*cos(lat2)*sin(lon2)
z = A*sin(lat1) + B*sin(lat2)
lat_rad=atan2(z,sqrt(x**2+y**2))
lon_rad=atan2(y,x)
lat_deg = lat_rad*180/pi
lon_deg = lon_rad*180/pi
print('%.2f' %f, '%.4f' %lat_deg, '%.4f' %lon_deg)
I use the np.arange() function to do a fractional iteration, f, between 0 (the starting point) and 1 (the destination).
The output of the for loop is:
0.00 33.9500 -118.4000
0.20 36.6040 -110.2685
0.40 38.6695 -101.6259
0.60 40.0658 -92.5570
0.80 40.7311 -83.2103
Where, the first number is the fraction (f); the second number is the latitude (lat_deg) and the third number is the longitude (lon_deg).
My question is: how do I convert the output of my code into a pandas (3x6) data frame with the data arranged in 3 columns with header Fraction (col1), Latitude (col2), Longitude (col3)?
Once the output is in a pandas data frame I can then easily write the data into a CSV file.
You're almost there. With the following modifications, you will be able to get your CSV:
Append your values to a list instead of printing them.
Convert the result to a dataframe
Below is your code with the required updates. I have now tested this and it works all the way to the final CSV.
import numpy as np
import pandas as pd
from math import radians, sin, cos, acos, atan2, sqrt, pi
# Numbers per your instructions
lat1 = radians(float(33.95))
lon1 = radians(float(-118.40))
lat2 = radians(float(40.6333))
lon2 = radians(float(-73.7833))
#Haversine formula to calculate the distance, in radians, between starting point and destination:
d = ((6371.01 * acos(sin(lat1)*sin(lat2) + cos(lat1)*cos(lat2)*cos(lon1 - lon2)))/1.852)/(180*60/pi)
x = np.arange(0, 1, 0.2)
# An empty list into which we'll append each list of values
res = []
for f in x:
A=sin((1-f)*d)/sin(d)
B=sin(f*d)/sin(d)
x = A*cos(lat1)*cos(lon1) + B*cos(lat2)*cos(lon2)
y = A*cos(lat1)*sin(lon1) + B*cos(lat2)*sin(lon2)
z = A*sin(lat1) + B*sin(lat2)
lat_rad=atan2(z,sqrt(x**2+y**2))
lon_rad=atan2(y,x)
lat_deg = lat_rad*180/pi
lon_deg = lon_rad*180/pi
# Add the desired values, creating a list of lists
res.append([f, lat_deg, lon_deg])
# Convert the result to a dataframe
res_df= pd.DataFrame(res, columns=['Fraction', 'Latitude', 'Longitude'])
# Voila! You can now save to CSV
res_df.to_csv('coordinates.csv', index=False)
I am writing a cuda kernel to convert rgba image to gray scale image in pycuda, here is the PyCUDA code:
import numpy as np
import matplotlib.pyplot as plt
import pycuda.autoinit
import pycuda.driver as cuda
from pycuda.compiler import SourceModule
kernel = SourceModule("""
#include <stdio.h>
__global__ void rgba_to_greyscale(const uchar4* const rgbaImage,
unsigned char* const greyImage,
int numRows, int numCols)
{
int y = threadIdx.y+ blockIdx.y* blockDim.y;
int x = threadIdx.x+ blockIdx.x* blockDim.x;
if (y < numCols && x < numRows) {
int index = numRows*y +x;
uchar4 color = rgbaImage[index];
unsigned char grey = (unsigned char)(0.299f*color.x+ 0.587f*color.y +
0.114f*color.z);
greyImage[index] = grey;
}
}
""")
However, the problem is how to relate uchar4* to numpy array. I know can modify my kernel function to accept int* or float*, and make it work. But I just wonder how to make the above kernel function to work in pycuda.
Below is host code.
def gpu_rgb2gray(image):
shape = image.shape
n_rows, n_cols, _ = np.array(shape, dtype=np.int)
image_gray = np.empty((n_rows, n_cols), dtype= np.int)
## HERE is confusing part, how to rearrange image to match unchar4* ??
image = image.reshape(1, -1, 4)
# Get kernel function
rgba2gray = kernel.get_function("rgba_to_greyscale")
# Define block, grid and compute
blockDim = (32, 32, 1) # 1024 threads in total
dx, mx = divmod(shape[1], blockDim[0])
dy, my = divmod(shape[0], blockDim[1])
gridDim = ((dx + (mx>0)), (dy + (my>0)), 1)
# Kernel function
# HERE doesn't work because of mismatch
rgba2gray (
cuda.In(image), cuda.Out(image_gray), n_rows, n_cols,
block=blockDim, grid=gridDim)
return image_gray
Anyone have any ideas? Thanks!
The gpuarray class has native support for CUDA's built in vector types (including uchar4).
So you can create as gpuarray instance with the correct dtype for the kernel, and copy the host image to that gpuarray using buffers, then use the gpuarray as the kernel input argument. As an example (and if I understood your code correctly), something like this should probably work:
import pycuda.gpuarray as gpuarray
....
def gpu_rgb2gray(image):
shape = image.shape
image_rgb = gpuarray.empty(shape, dtype=gpuarray.vec.uchar4)
cuda.memcpy_htod(image_rgb.gpudata, image.data)
image_gray = gpuarray.empty(shape, dtype=np.uint8)
# Get kernel function
rgba2gray = kernel.get_function("rgba_to_greyscale")
# Define block, grid and compute
blockDim = (32, 32, 1) # 1024 threads in total
dx, mx = divmod(shape[1], blockDim[0])
dy, my = divmod(shape[0], blockDim[1])
gridDim = ((dx + (mx>0)), (dy + (my>0)), 1)
rgba2gray ( image_rgb, image_gray, np.int32(shape[0]), np.int32(shape[1]), block=blockDim, grid=gridDim)
img_gray = np.array(image_gray.get(), dtype=np.int)
return img_gray
this would take an image of 32 bit unsigned integers and copy them to an array of uchar4 on the GPU and then upcast the resulting array of uchar back to integers on the device.
I'm trying to copy the Scipy Cookbook function:
from scipy import ogrid, sin, mgrid, ndimage, array
x,y = ogrid[-1:1:5j,-1:1:5j]
fvals = sin(x)*sin(y)
newx,newy = mgrid[-1:1:100j,-1:1:100j]
x0 = x[0,0]
y0 = y[0,0]
dx = x[1,0] - x0
dy = y[0,1] - y0
ivals = (newx - x0)/dx
jvals = (newy - y0)/dy
coords = array([ivals, jvals])
newf = ndimage.map_coordinates(fvals, coords)
by using my own function that has to work for many scenarios
import scipy
import numpy as np
"""N-D interpolation for equally-spaced data"""
x = np.c_[plist['modx']]
y = np.transpose(np.c_[plist['mody']])
pdb.set_trace()
#newx,newy = np.meshgrid(plist['newx'],plist['newy'])
newx,newy = scipy.mgrid[plist['modx'][0]:plist['modx'][-1]:-plist['remapto'],
plist['mody'][0]:plist['mody'][-1]:-plist['remapto']]
x0 = x[0,0]
y0 = y[0,0]
dx = x[1,0] - x0
dy = y[0,1] - y0
ivals = (newx - x0)/dx
jvals = (newy - y0)/dy
coords = scipy.array([ivals, jvals])
for i in np.arange(ivals.shape[0]):
nvals[i] = scipy.ndimage.map_coordinates(ivals[i], coords)
I'm having difficulty getting this code to work properly. The problem areas are:
1.) Recreating this line: newx,newy = mgrid[-1:1:100j,-1:1:100j]. In my case I have a dictionary with the grid in vector form. I've tried to recreate this line using np.meshgrid but then I get an error on line coords = scipy.array([ivals, jvals]). I'm looking for some help in recreating this Cookbook function and making it more dynamic
any help is greatly appreciated.
/M
You should have a look at the documentation for map_coordinates. I don't see where the actual data you are trying to interpolate is in your code. What I mean is, presumably you have some data input which is a function of x and y; i.e. input = f(x,y) that you want to interpolate. In the first example you show, this is the array fvals. This should be your first argument to map_coordinates.
For example, if the data you are trying to inperpolate is input, which should be a 2-dimensional array of shape (len(x),len(y)), then the interpolated data would be:
interpolated_data = map_coordinates(input, coords)