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Added machine learning tools #59

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merged 3 commits into from
Feb 7, 2022
Merged

Added machine learning tools #59

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7d1c16a
Added machine learning tools
giswqs Feb 3, 2022
29a3f2d
Update datasets / vignette
brownag Feb 4, 2022
beef70a
Add wbt_ prefix to function names to match R exports
brownag Feb 4, 2022
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -10,3 +10,4 @@ whiteboxR.Rproj
.vscode/
/doc/
/Meta/
*.zip
51 changes: 30 additions & 21 deletions PY2R/automation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,8 @@
import urllib.request

# Extract function header


def function_header(line):
if line.startswith("def"):
line = line.replace("self, i,", "input,")
Expand All @@ -45,7 +47,7 @@ def function_header(line):
# Extract function name
def function_name(line):
line = line.strip()
name = line[0 : line.find("(")]
name = line[0: line.find("(")]
return name


Expand All @@ -61,7 +63,7 @@ def is_float(string):
# Generate R function block
def function_block(line, ff):
line = line.strip()
function_name = line[0 : line.find("(")]
function_name = line[0: line.find("(")]
start = line.find("(") + 1
end = len(line) - 1
argument = line[start:end]
Expand All @@ -74,7 +76,8 @@ def function_block(line, ff):
item = item.strip()
if "=" not in item:
ff.write(
' args <- paste(args, paste0("--' + item + '=", ' + item + "))" + "\n"
' args <- paste(args, paste0("--' + item +
'=", ' + item + "))" + "\n"
)
elif "verbose" in item:
continue
Expand Down Expand Up @@ -184,7 +187,8 @@ def function_example(fun_name):
duplicate_problems.append("lidar_block_maximum")
duplicate_problems.append("flightline_overlap")
if fun_name in duplicate_problems:
example = example.replace("--input=file.las --output=outfile.tif", "", 1)
example = example.replace(
"--input=file.las --output=outfile.tif", "", 1)
example = example.replace("--palette=light_quant.plt", "")

if fun_name == "k_nearest_mean_filter":
Expand Down Expand Up @@ -220,6 +224,7 @@ def function_example(fun_name):
"# Hydrological Analysis #": "hydro_analysis.R",
"# Image Processing Tools #": "image_analysis.R",
"# LiDAR Tools #": "lidar_analysis.R",
"# Machine Learning #": "machine_learning.R",
"# Math and Stats Tools #": "math_stat_analysis.R",
"# Precision Agriculture #": "precision_agriculture.R",
"# Stream Network Analysis #": "stream_network_analysis.R",
Expand Down Expand Up @@ -262,7 +267,8 @@ def function_example(fun_name):

# Create an R script for each toolbox
if line in toolboxes:
script_path = os.path.join(dir_path, "scripts", toolboxes[line])
script_path = os.path.join(
dir_path, "scripts", toolboxes[line])
ff = open(script_path, "w")
print(script_path)

Expand Down Expand Up @@ -316,7 +322,7 @@ def function_example(fun_name):
if add_example:
fun_name = function_name(fun_head)
wbt_fun_name = "wbt_" + fun_name
fun_params = fun_head[fun_head.index("(") :]
fun_params = fun_head[fun_head.index("("):]

if (fun_params == "(input, output, verbose_mode=FALSE)") and (
fun_name != "raster_histogram"
Expand Down Expand Up @@ -346,25 +352,28 @@ def function_example(fun_name):
ff.write("#' }\n")
# print(line1)
# print(line2)

skip_fun_tests = ["raster_histogram", "attribute_correlation",
"conditional_evaluation", "crispness_index",
"ks_test_for_normality", "rescale_value_range", "trend_surface"]
if (fun_params.startswith("(input, output") and not any(fun_name in s for s in skip_fun_tests)):
# write test scripts
test_file_name = "test-" + wbt_fun_name + ".R"
test_file_path = os.path.join(dir_path, "tests", test_file_name)
f = open(test_file_path, "w")
f.write('context("{}")\n\n'.format(wbt_fun_name))
f.write('test_that("' + desc + '", {\n\n')
f.write(" skip_on_cran()\n")
f.write(" skip_if_not(check_whitebox_binary())\n")
f.write(' dem <- system.file("extdata", "DEM.tif", package = "whitebox")\n')
f.write(' ret <- {}(input = dem, output = "output.tif")\n'.format(wbt_fun_name))
f.write(' expect_match(ret, "Elapsed Time")\n\n')
f.write("})\n")
print(test_file_path)
f.close()
# write test scripts
test_file_name = "test-" + wbt_fun_name + ".R"
test_file_path = os.path.join(
dir_path, "tests", test_file_name)
f = open(test_file_path, "w")
f.write('context("{}")\n\n'.format(wbt_fun_name))
f.write('test_that("' + desc + '", {\n\n')
f.write(" skip_on_cran()\n")
f.write(" skip_if_not(check_whitebox_binary())\n")
f.write(
' dem <- system.file("extdata", "DEM.tif", package = "whitebox")\n')
f.write(
' ret <- {}(input = dem, output = "output.tif")\n'.format(wbt_fun_name))
f.write(' expect_match(ret, "Elapsed Time")\n\n')
f.write("})\n")
print(test_file_path)
f.close()

# fun_name = function_name(fun_head)
# example = function_example(fun_name)
Expand Down
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