landcover_subindicator: land

annotate land_cover.py @ 0:828c02027180 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15

author	ecology
date	Mon, 21 Oct 2024 16:47:10 +0000
parents
children

rev	line source
0 828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	1 # Land Cover TE Algorithm Without GEE
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	2
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	3 # How to Execute:
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	4 # - Load the two images (.TIFF) of the rasters
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	5 # to be processed in the "/data/land_cover/input" folder
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	6 # - Setting the two filenames in the specific cell of this script (0)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	7 # - Run all cells of the script
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	8 # - Check the script results in the "/data/land_cover/output" folder
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	9 # - Land Cover Degradation "/data/land_cover/output/lc_dg.tiff"
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	10 # - Land Cover Transition "/data/land_cover/output/lc_tr.tiff"
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	11
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	12 # Librairies import
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	13 import argparse
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	14 import json
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	15 import os
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	16 import sys
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	17
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	18 import matplotlib.pyplot as plt
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	19
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	20 import numpy as np
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	21
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	22 import rasterio
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	23 from rasterio.plot import show
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	24
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	25 from te_schemas.land_cover import LCLegendNesting
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	26 from te_schemas.land_cover import LCTransitionDefinitionDeg
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	27
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	28 # Methods to manage Rasters
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	29
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	30
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	31 def remap(raster, problem_numbers, alternative_numbers):
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	32 n_min, n_max = raster.min(), raster.max()
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	33 replacer = np.arange(n_min, n_max + 1)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	34 mask = (problem_numbers >= n_min) & (problem_numbers <= n_max)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	35 replacer[problem_numbers[mask] - n_min] = alternative_numbers[mask]
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	36 raster_replaced = replacer[raster - n_min]
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	37 return raster_replaced
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	38
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	39
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	40 def saveRaster(dataset, datasetPath, cols, rows, projection, namedataset=None):
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	41 if namedataset:
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	42 rasterSet = rasterio.open(datasetPath,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	43 'w',
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	44 driver='GTiff',
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	45 height=rows,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	46 width=cols,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	47 count=1,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	48 dtype=np.int8,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	49 crs=projection,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	50 transform=transform, )
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	51 rasterSet.write(dataset, 1)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	52 rasterSet.close()
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	53 else:
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	54 rasterSet = rasterio.open(datasetPath,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	55 'w',
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	56 driver='GTiff',
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	57 height=rows,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	58 width=cols,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	59 count=1,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	60 dtype=np.int8,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	61 crs=projection,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	62 transform=transform, )
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	63 rasterSet.write(dataset, 1)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	64 rasterSet.set_band_description(1, namedataset)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	65 rasterSet.close()
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	66
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	67
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	68 def plot(ndviImage, cmap):
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	69 src = rasterio.open(ndviImage, 'r')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	70 fig, ax = plt.subplots(1, figsize=(12, 12))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	71 show(src, cmap=cmap, ax=ax)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	72 ax.set_xlabel('Est')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	73 ax.set_ylabel('Nord')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	74 plt.show()
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	75
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	76
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	77 def plotContour(ndviImage, cmap):
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	78 src = rasterio.open(ndviImage, 'r')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	79 fig, ax = plt.subplots(1, figsize=(12, 12))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	80 show(src, cmap=cmap, contour=True, ax=ax)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	81 ax.set_xlabel('Est')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	82 ax.set_ylabel('Nord')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	83 plt.show()
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	84
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	85
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	86 # Setting inputs
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	87 command_line_args = sys.argv[1:]
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	88
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	89
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	90 parser = argparse.ArgumentParser(description="landcover inputs and outputs")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	91 # Add arguments
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	92 parser.add_argument("--raster_1", help="raster 1")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	93 parser.add_argument("--raster_2", help="raster 2")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	94 parser.add_argument("--json", help="json")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	95
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	96 args = parser.parse_args(command_line_args)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	97
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	98 # Parse the command line arguments
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	99
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	100 # Import data
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	101
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	102 path_raster_yi = args.raster_1
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	103 path_raster_yf = args.raster_2
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	104 fjson = args.json
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	105 # Input Rasters
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	106
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	107 # Outputs
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	108 out_dir = os.path.join(os.getcwd(), "data/land_cover/output/")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	109 if not os.path.exists(out_dir):
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	110 os.makedirs(out_dir)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	111
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	112 # Output Rasters
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	113 path_lc_tr = os.path.join(out_dir, 'lc_tr.tiff')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	114 path_lc_bl = os.path.join(out_dir, 'lc_bl.tiff')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	115 path_lc_dg = os.path.join(out_dir, 'lc_dg.tiff')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	116 path_lc_tg = os.path.join(out_dir, 'lc_tg.tiff')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	117 path_change_yf_yi = os.path.join(out_dir, 'change_yf_yi.tiff')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	118 path_lc_baseline_esa = os.path.join(out_dir, 'lc_baseline_esa.tiff')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	119 path_lc_target_esa = os.path.join(out_dir, 'lc_target_esa.tiff')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	120 path_out_img = os.path.join(out_dir, 'stack.tiff')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	121
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	122 # Contours
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	123 contours_change_yf_yi = os.path.join(out_dir, '/change_yf_yi0.shp')
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	124
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	125
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	126 # Parsing Inputs
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	127 # Load static inputs
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	128 # Transition Matrix, ESA Legend, IPCC Legend
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	129 # Input Raster and Vector Paths
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	130 params = json.load(open(fjson))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	131
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	132 crs = params.get("crs")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	133
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	134 trans_matrix_val = params.get("trans_matrix")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	135 trans_matrix = LCTransitionDefinitionDeg.Schema().load(trans_matrix_val)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	136
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	137 esa_to_custom_nesting = LCLegendNesting.Schema().load(
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	138 params.get("legend_nesting_esa_to_custom")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	139 )
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	140
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	141 ipcc_nesting = LCLegendNesting.Schema().load(
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	142 params.get("legend_nesting_custom_to_ipcc")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	143 )
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	144
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	145 class_codes = sorted([c.code for c in esa_to_custom_nesting.parent.key])
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	146 class_positions = [*range(1, len(class_codes) + 1)]
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	147
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	148 # Load dynamic inputs
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	149 # Baseline ESA Raster
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	150 raster_yi = rasterio.open(path_raster_yi)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	151 lc_baseline_esa = raster_yi.read(1)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	152 yi_dict_profile = dict(raster_yi.profile)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	153
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	154 for k in yi_dict_profile:
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	155 print(k.upper(), yi_dict_profile[k])
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	156
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	157 # Target ESA Raster
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	158 raster_yf = rasterio.open(path_raster_yf)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	159 lc_target_esa = raster_yf.read(1)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	160 yf_dict_profile = dict(raster_yf.profile)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	161
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	162 for k in yf_dict_profile:
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	163 print(k.upper(), yf_dict_profile[k])
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	164
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	165 cols = raster_yi.width
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	166 rows = raster_yf.height
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	167 transform = raster_yi.transform
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	168 projection = raster_yi.crs
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	169
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	170 # Setting up output
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	171 saveRaster(lc_baseline_esa.astype('int8'),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	172 path_lc_baseline_esa,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	173 cols,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	174 rows,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	175 projection,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	176 "Land_cover_yi")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	177
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	178 saveRaster(lc_target_esa.astype('int8'),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	179 path_lc_target_esa,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	180 cols,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	181 rows,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	182 projection,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	183 "Land_cover_yf")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	184
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	185 # Algorithm execution
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	186 # Transition codes are based on the class code indices
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	187 # (i.e. their order when sorted by class code) -
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	188 # not the class codes themselves.
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	189 # So need to reclass the land cover used for the transition calculations
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	190 # from the raw class codes to the positional indices of those class codes.
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	191 # And before doing that, need to reclassified initial and
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	192 # final layers to the IPCC (or custom) classes.
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	193
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	194 # Processing baseline raster
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	195 bl_remap_1 = remap(lc_baseline_esa,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	196 np.asarray(esa_to_custom_nesting.get_list()[0]),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	197 np.asarray(esa_to_custom_nesting.get_list()[1]))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	198 lc_bl = remap(bl_remap_1, np.asarray(class_codes), np.asarray(class_positions))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	199
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	200 saveRaster(lc_bl.astype('int8'),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	201 path_lc_bl,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	202 cols,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	203 rows,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	204 projection,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	205 "Land_cover_yi")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	206
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	207 # Processing Target Raster
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	208 tg_remap_1 = remap(lc_target_esa,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	209 np.asarray(esa_to_custom_nesting.get_list()[0]),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	210 np.asarray(esa_to_custom_nesting.get_list()[1]))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	211 lc_tg = remap(tg_remap_1, np.asarray(class_codes), np.asarray(class_positions))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	212
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	213 saveRaster(lc_tg.astype('int8'),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	214 path_lc_tg,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	215 cols,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	216 rows,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	217 projection,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	218 "Land_cover_yf")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	219
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	220 # Processing Transition Map
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	221 # Compute transition map (first digit for baseline land cover,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	222 # and second digit for target year land cover)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	223 lc_tr = (lc_bl * esa_to_custom_nesting.parent.get_multiplier()) + lc_tg
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	224
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	225 # Compute land cover transition
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	226 # Remap persistence classes so they are sequential.
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	227 # This makes it easier to assign a clear color ramp in QGIS.
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	228 lc_tr_pre_remap = remap(lc_tr,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	229 np.asarray(trans_matrix.get_persistence_list()[0]),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	230 np.asarray(trans_matrix.get_persistence_list()[1]))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	231
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	232 saveRaster(lc_tr_pre_remap.astype('int8'),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	233 path_lc_tr,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	234 cols,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	235 rows,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	236 projection,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	237 "Land_cover_transitions_yi-yf")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	238
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	239 # Compute land cover degradation
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	240 # definition of land cover transitions as degradation (-1),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	241 # improvement (1), or no relevant change (0)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	242 lc_dg = remap(lc_tr,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	243 np.asarray(trans_matrix.get_list()[0]),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	244 np.asarray(trans_matrix.get_list()[1]))
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	245
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	246 saveRaster(lc_dg.astype('int8'),
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	247 path_lc_dg,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	248 cols,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	249 rows,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	250 projection,
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	251 "Land_cover_degradation")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	252
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	253 # Compute Mutlibands stack
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	254 # Land Cover Degradation + Baseline ESA
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	255 # + Target ESA + Land Cover Transition
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	256 dg_raster = rasterio.open(path_lc_dg, "r")
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	257 dg = dg_raster.read(1, masked=True)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	258 baseline_esa = rasterio.open(path_lc_baseline_esa, "r").read(1, masked=True)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	259 target_esa = rasterio.open(path_lc_target_esa, "r").read(1, masked=True)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	260 tr = rasterio.open(path_lc_tr, "r").read(1, masked=True)
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	261
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	262 band_list = [dg, lc_baseline_esa, lc_target_esa, tr]
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	263 out_meta = dg_raster.meta.copy()
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	264 out_meta.update({"count": 4})
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	265
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	266 with rasterio.open(path_out_img, 'w', **out_meta) as dest:
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	267 for band_nr, src in enumerate(band_list, start=1):
828c02027180 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/earth commit 4cbace8c3a71b7a1638cfd44a21f5d4b84d2fd15 ecology parents: diff changeset	268 dest.write(src, band_nr)

Mercurial > repos > ecology > landcover_subindicator

annotate land_cover.py @ 0:828c02027180 draft default tip