mirror of
https://github.com/rasterio/rasterio.git
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Yo, I hear you like parentheses...
Old syntax traded in for an easy to parse lisp-like syntax. No need for a temporary variable and much more secure.
This commit is contained in:
Sean Gillies
parent
c6d8bfeb17
commit
5dbcc6f40f
@ -8,7 +8,7 @@ import sys
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import warnings
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import click
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from cligj import files_inout_arg
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import parsnip
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import rasterio
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from rasterio.rio.cli import cli
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@ -22,6 +22,9 @@ from rasterio.rio.cli import cli
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type=click.Path(resolve_path=False),
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required=True,
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metavar="INPUTS... OUTPUT")
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@click.option('--name', multiple=True,
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help='Specify an input file with a unique short (alphas only) name '
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'for use in commands like "a=tests/data/RGB.byte.tif".')
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@click.option('--dtype',
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type=click.Choice([
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'ubyte', 'uint8', 'uint16', 'int16', 'uint32',
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@ -29,23 +32,44 @@ from rasterio.rio.cli import cli
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default='float64',
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help="Output data type (default: float64).")
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@click.pass_context
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def calc(ctx, command, files, dtype):
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def calc(ctx, command, files, name, dtype):
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"""A raster data calculator
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Applies one or more commands to a set of input datasets and writes
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the results to a new dataset.
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Evaluates an expression using input datasets and writes the result
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to a new dataset.
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Command syntax is a work in progress. Currently:
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* {n} represents the n-th input dataset (a 3-D array)
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* {n,m} represents the m-th band of the n-th dataset (a 2-D array).
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* Standard numpy array operators (+, -, *, /) are available.
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* Multiple commands delimited by ; may be executed.
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* The result of the previous command is represented by {}.
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* When the final result is a tuple of arrays, a multi band output
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file is written.
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* When the final result is a single array, a single band output
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file is written.
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Command syntax is lisp-like. An expression consists of an operator
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or function name and one or more strings, numbers, or expressions
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enclosed in parentheses. Functions include ``ra`` (gets a raster
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array) and ``list`` (makes a list of arrays).
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\b
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* (ra i) evaluates to the i-th input dataset (a 3-D array).
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* (ra i j) evaluates to the j-th band of the i-th dataset (a 2-D
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array).
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* (ra foo j) evaluates to the j-th band of a dataset named foo (see
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help on the --name option above).
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* Standard numpy array operators (+, -, *, /) are available.
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* When the final result is a list of arrays, a multi band output
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file is written.
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* When the final result is a single array, a single band output
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file is written.
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Example:
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\b
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$ rio calc "(+ (* (ra 1) 0.95) 2)" tests/data/RGB.byte.tif \\
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> /tmp/out.tif --dtype ubyte
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Produces a 3-band GeoTIFF with all values scaled by 0.95 and
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incremented by 2.
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\b
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$ rio calc "(list (+ (ra 1) 125) (ra 1) (ra 1))" \\
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> tests/data/shade.tif /tmp/out.tif --dtype ubyte
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Produces a 3-band RGB GeoTIFF, with red levels incremented by 125,
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from the single-band input.
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"""
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import numpy as np
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@ -56,74 +80,34 @@ def calc(ctx, command, files, dtype):
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try:
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with rasterio.drivers(CPL_DEBUG=verbosity>2):
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output = files[-1]
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files = files[:-1]
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with rasterio.open(files[0]) as first:
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inputs = (
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[tuple(n.split('=')) for n in name] +
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[(None, n) for n in files[:-1]])
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with rasterio.open(inputs[0][1]) as first:
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kwargs = first.meta
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kwargs['transform'] = kwargs.pop('affine')
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kwargs['dtype'] = dtype
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names = []
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sources = []
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for path in files:
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ctxkwds = {}
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for name, path in inputs:
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with rasterio.open(path) as src:
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names.append(src.name)
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# Using the class method instead of instance method.
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# Latter raises
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#
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# TypeError: astype() got an unexpected keyword argument 'copy'
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# Possibly something to do with the instance being a masked
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#
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# possibly something to do with the instance being a masked
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# array.
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sources.append(
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np.ndarray.astype(src.read(), 'float64', copy=False))
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ctxkwds[name or src.name] = np.ndarray.astype(
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src.read(), 'float64', copy=False)
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#sources = np.ma.asanyarray([s for s in sources])
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with parsnip.ctx(**ctxkwds):
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res = parsnip.handleLine(command)
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parts = command.split(';')
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_prev = None
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def cmd_sources(match):
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text = match.group(1)
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parts = text.split(',')
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v = parts.pop(0)
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if v in names:
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a = names.index(v)
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s = 'sources[%d]' % a
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if parts:
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s += '[%d]' % (int(parts.pop(0)) - 1)
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return s
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for part in filter(lambda p: p.strip(), parts):
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# TODO: implement a real parser for calc expressions,
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# perhaps using numexpr's parser as a guide, instead
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# eval'ing any string.
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# Translate '{}' to '_prev'.
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cmd = re.sub(r'{}', '_prev', part)
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cmd = re.sub(
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r'{(\d+),(\d+)}',
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lambda m: 'sources[%d][%d]' % (
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int(m.group(1))-1,
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int(m.group(2))-1),
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cmd)
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cmd = re.sub(
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r'{(\d+)}',
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lambda m: 'sources[%d]' % (int(m.group(1))-1),
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cmd)
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cmd = re.sub(r'{(.+)}', cmd_sources, cmd)
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logger.debug("Translated cmd: %r", cmd)
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res = eval(cmd)
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_prev = res
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if isinstance(res, tuple) or len(res.shape) == 3:
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results = np.asanyarray([
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np.ndarray.astype(r, dtype, copy=False
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) for r in res])
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if len(res.shape) == 3:
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results = np.ndarray.astype(res, dtype, copy=False)
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else:
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results = np.asanyarray(
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[np.ndarray.astype(res, dtype, copy=False)])
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@ -5,6 +5,7 @@ cython>=0.20
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delocate
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enum34
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numpy>=1.8.0
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git+git://github.com/mapbox/parsnip#egg=parsnip
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pytest
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setuptools>=0.9.8
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wheel
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@ -2,4 +2,5 @@ affine
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cligj
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enum34
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numpy>=1.8.0
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parsnip
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setuptools
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3
setup.py
3
setup.py
@ -169,7 +169,8 @@ with open('README.rst') as f:
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inst_reqs = [
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'affine>=1.0',
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'cligj',
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'Numpy>=1.7' ]
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'Numpy>=1.7',
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'parsnip']
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if sys.version_info < (3, 4):
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inst_reqs.append('enum34')
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@ -14,7 +14,7 @@ def test_err(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'0.10*{1}.upper()', 'tests/data/shade.tif', outfile],
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'(& 0.1 (ra 1))', 'tests/data/shade.tif', outfile],
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catch_exceptions=False)
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assert result.exit_code == 1
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@ -23,7 +23,7 @@ def test_multiband_calc(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'0.10*{1} + 125', 'tests/data/shade.tif', outfile],
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'(+ 125 (* 0.1 (ra 1)))', 'tests/data/shade.tif', outfile],
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catch_exceptions=False)
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assert result.exit_code == 0
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with rasterio.open(outfile) as src:
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@ -33,11 +33,13 @@ def test_multiband_calc(tmpdir):
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assert data.min() == 125
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def test_singleband_calc(tmpdir):
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def test_singleband_calc_byindex(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'0.10*{1,1} + 125', 'tests/data/shade.tif', outfile],
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'(+ 125 (* 0.1 (ra 1 1)))',
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'tests/data/shade.tif',
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outfile],
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catch_exceptions=False)
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assert result.exit_code == 0
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with rasterio.open(outfile) as src:
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@ -47,12 +49,12 @@ def test_singleband_calc(tmpdir):
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assert data.min() == 125
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def test_singleband_calc_by_name(tmpdir):
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def test_singleband_calc_byname(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'0.10*{tests/data/shade.tif,1} + 125',
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'tests/data/shade.tif',
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'(+ 125 (* 0.1 (ra shade 1)))',
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'--name', 'shade=tests/data/shade.tif',
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outfile],
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catch_exceptions=False)
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assert result.exit_code == 0
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@ -69,7 +71,7 @@ def test_parts_calc(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'({1,1} + 125, {1,1}, {1,1})',
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'(list (+ (ra 1 1) 125) (ra 1 1) (ra 1 1))',
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'--dtype', 'uint8',
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'tests/data/shade.tif',
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outfile],
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@ -89,7 +91,7 @@ def test_parts_calc_2(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'({1,1} + {1,2} + {1,3})/3',
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'(+ (+ (/ (ra 1 1) 3) (/ (ra 1 2) 3)) (/ (ra 1 3) 3))',
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'--dtype', 'uint8',
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'tests/data/RGB.byte.tif',
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outfile],
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@ -102,64 +104,11 @@ def test_parts_calc_2(tmpdir):
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assert round(data.mean(), 1) == 60.3
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def test_parts_calc_tempval(tmpdir):
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# Produce greyscale output from the RGB file.
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'{1,1}; {} + {1,2}; {} + {1,3}; {}; ({}/3)',
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'--dtype', 'uint8',
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'tests/data/RGB.byte.tif',
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outfile],
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catch_exceptions=False)
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assert result.exit_code == 0
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with rasterio.open(outfile) as src:
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assert src.count == 1
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assert src.meta['dtype'] == 'uint8'
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data = src.read()
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assert round(data.mean(), 1) == 60.3
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def test_copy_rgb(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'{1}',
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'--dtype', 'uint8',
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'tests/data/RGB.byte.tif',
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outfile],
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catch_exceptions=False)
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assert result.exit_code == 0
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with rasterio.open(outfile) as src:
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assert src.count == 3
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assert src.meta['dtype'] == 'uint8'
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data = src.read()
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assert round(data.mean(), 1) == 60.6
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def test_copy_rgb_tempval(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'{1}; {}',
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'--dtype', 'uint8',
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'tests/data/RGB.byte.tif',
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outfile],
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catch_exceptions=False)
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assert result.exit_code == 0
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with rasterio.open(outfile) as src:
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assert src.count == 3
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assert src.meta['dtype'] == 'uint8'
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data = src.read()
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assert round(data.mean(), 1) == 60.6
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def test_copy_rgb_by_name(tmpdir):
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outfile = str(tmpdir.join('out.tif'))
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runner = CliRunner()
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result = runner.invoke(calc, [
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'{tests/data/RGB.byte.tif}',
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'(ra 1)',
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'--dtype', 'uint8',
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'tests/data/RGB.byte.tif',
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outfile],
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