def plot_points(multidateraster, pointfile, startdoy, doyinterval):
"""
"""
import os
from utils import unique_name
from plotting import PixelPlot
from core import pixel as pixelObject
from vectorFunctions import get_px_coords_from_shapefile
from imageFunctions import openImage
outpath = unique_name(os.path.dirname(multidateraster), "plots", ext=".pdf", usetime=True)
coords = get_px_coords_from_shapefile(multidateraster, pointfile)
plot = PixelPlot(os.path.dirname(outpath), os.path.basename(outpath))
raster = openImage(multidateraster)
for coord in coords:
pixel = pixelObject(coord[0], coord[1])
pixel.get_pixel_values(raster, startdoy, doyinterval)
plot.add_pixel(pixel, closefigure=True)
plot.close_plot()
raster = None
def refile_error(self, src):
# TODO: errors should be a Filer
# and moved elsewhere. Perhaps FilerMaster should
# override refile_error and use FilerError to refile
root, ext = os.path.splitext(src)
dst = os.path.join(self.files_path, self.err_dir,
os.path.basename(src))
if os.path.exists(dst):
dst = utils.unique_name(dst)
try:
self.refile(src, dsts=[dst], op='mv')
except Exception as e:
self.logger.error(e)
def refile_error(self,src): # TODO: errors should be a Filer # and moved elsewhere. Perhaps FilerMaster should # override refile_error and use FilerError to refile root,ext = os.path.splitext(src) dst = os.path.join( self.files_path, self.err_dir, os.path.basename(src) ) if os.path.exists(dst): dst = utils.unique_name(dst) try: self.refile(src,dsts=[dst],op='mv') except Exception as e: self.logger.error(e)
def show_binary(self, data, mimetype):
import tempfile
prog = config.MIME_HELPER.get(mimetype)
if not prog:
raise Interface.Aborted("Cannot display to a terminal: %s" % mimetype)
fp = tempfile.NamedTemporaryFile(prefix=unique_name('view'), dir=config.TMP_DIR)
fp.write(data)
fp.flush()
cmdline = prog % fp.name
status = os.WEXITSTATUS(os.system(cmdline))
fp.close()
if status:
raise Interface.Aborted("Viewer aborted: (%04x) %r" % (status, cmdline))
return
def show_binary(self, data, mimetype):
import tempfile
prog = config.MIME_HELPER.get(mimetype)
if not prog:
raise Interface.Aborted("Cannot display to a terminal: %s" %
mimetype)
fp = tempfile.NamedTemporaryFile(prefix=unique_name('view'),
dir=config.TMP_DIR)
fp.write(data)
fp.flush()
cmdline = prog % fp.name
status = os.WEXITSTATUS(os.system(cmdline))
fp.close()
if status:
raise Interface.Aborted("Viewer aborted: (%04x) %r" %
(status, cmdline))
return
def __rename_with_md5(self, path):
new_path = utils.unique_name(path, self.custom_config.md5_len,
self.custom_config.md5_concat_by)
if new_path is None:
return None
(parent_path, new_file_name) = os.path.split(new_path)
if new_file_name.startswith('basic'):
logger.debug('%s %s %s' % (path, parent_path,new_file_name))
#TODO
#[x] Rename
if self.custom_config.delete_source:
os.rename(path, new_path)
else:
shutil.copy(path, new_path)
return new_file_name
def plot_sigs(signaturedirectory, outputdirectory, name, signaturename):
"""
"""
import os
from utils import find_files, unique_name
from core import signatureCollection
from plotting import SignaturePlot
if not outputdirectory:
outputdirectory = signaturedirectory
sigs = find_files(signaturedirectory, "mean.ref")
if not sigs:
click.BadParameter("Did not find any signature files in the specified directory.")
if signaturename:
filteredsigs = []
for searchstring in signaturename:
for sig in sigs:
if searchstring.upper() in sig.upper():
filteredsigs.append(sig)
sigs = filteredsigs
signatures = signatureCollection()
for sig in sigs:
try:
signatures.add(sig)
except Exception as e:
print e
#TODO Fix core temporalSignature to use exceptions so they can be properly handled here
name, ext = os.path.splitext(name)
path = unique_name(outputdirectory, name, ext=ext)
print("Outputting to {0}".format(path))
plot = SignaturePlot(outputdirectory, os.path.basename(path))
plot.plot_collection(signatures)
def edit_text(self, kernel, data, original=None):
import stat
def modtime(fname):
return os.stat(fname)[stat.ST_MTIME]
fname = os.path.join(config.TMP_DIR, unique_name('edit'))
fp = file(fname, 'wb')
fp.write(self.to_terminal(data))
fp.close()
t0 = modtime(fname)
cmdline = config.EDITOR % fp.name
status = os.WEXITSTATUS(os.system(cmdline))
if config.CHECK_EDITOR_STATUS and status:
raise Interface.Aborted("Editor aborted: (%04x) %r" % (status, cmdline))
if modtime(fname) <= t0:
raise Interface.Cancelled("Edit cancelled.")
fp = file(fname, 'rb')
data = self.from_terminal(fp.read())
fp.close()
kernel.submit_message(data, original)
return
def __init__(self,
dataset_path,
dataset_where_sql=None,
view_name=None,
force_nonspatial=False):
"""Initialize instance.
Args:
dataset_path (str): Path of the dataset.
dataset_where_sql (str): SQL where-clause for dataset
subselection.
view_name (str): Name of the view to create.
force_nonspatial (bool): Flag that forces a nonspatial view.
"""
self.name = view_name if view_name else unique_name('view')
self.dataset_path = dataset_path
self.dataset_meta = dataset_metadata(dataset_path)
self.is_spatial = all(
(self.dataset_meta['is_spatial'], not force_nonspatial))
self._where_sql = dataset_where_sql
def edit_text(self, kernel, data, original=None):
import stat
def modtime(fname):
return os.stat(fname)[stat.ST_MTIME]
fname = os.path.join(config.TMP_DIR, unique_name('edit'))
fp = file(fname, 'wb')
fp.write(self.to_terminal(data))
fp.close()
t0 = modtime(fname)
cmdline = config.EDITOR % fp.name
status = os.WEXITSTATUS(os.system(cmdline))
if config.CHECK_EDITOR_STATUS and status:
raise Interface.Aborted("Editor aborted: (%04x) %r" %
(status, cmdline))
if modtime(fname) <= t0:
raise Interface.Cancelled("Edit cancelled.")
fp = file(fname, 'rb')
data = self.from_terminal(fp.read())
fp.close()
kernel.submit_message(data, original)
return
def extract_signatures(image, shapefiledirectory, startdoy, doyinterval, outputdir, filelabel, plotsigs):
"""
Extracts temporal signatures for a set of point geometry shapefiles in a specified directory and outputs them to a
set of .ref files in an output directory.
"""
import os
from plotting import SignaturePlot
from utils import find_files, create_output_dir, unique_name
from signatureFunctions import get_sigs_in_dir, get_reference_curves
if outputdir is None:
outputdir = create_output_dir(os.path.dirname(image), "signatures", usetime=True)
shapefiles = find_files(shapefiledirectory, ".shp", recursive=False)
#TODO: Need a method to find only valid shapefiles in the directory
get_reference_curves(image, shapefiles, startdoy, doyinterval, outdir=outputdir, filepostfix=filelabel)
if plotsigs:
path = unique_name(outputdir, "signaturePlot", ext=".pdf")
sigs = get_sigs_in_dir(outputdir)
plot = SignaturePlot(outputdir, os.path.basename(path))
plot.plot_collection(sigs)
def _interpolate_c_kernel(self, expression, to_pts, to_element, fs, coords):
"""Produce a :class:`PyOP2.Kernel` from the c expression provided."""
coords_space = coords.function_space()
coords_element = coords_space.fiat_element
names = {v[0] for v in expression._user_args}
X = coords_element.tabulate(0, to_pts).values()[0]
# Produce C array notation of X.
X_str = "{{"+"},\n{".join([",".join(map(str, x)) for x in X.T])+"}}"
A = utils.unique_name("A", names)
X = utils.unique_name("X", names)
x_ = utils.unique_name("x_", names)
k = utils.unique_name("k", names)
d = utils.unique_name("d", names)
i_ = utils.unique_name("i", names)
# x is a reserved name.
x = "x"
if "x" in names:
raise ValueError("cannot use 'x' as a user-defined Expression variable")
ass_exp = [ast.Assign(ast.Symbol(A, (k,), ((len(expression.code), i),)),
ast.FlatBlock("%s" % code))
for i, code in enumerate(expression.code)]
vals = {
"X": X,
"x": x,
"x_": x_,
"k": k,
"d": d,
"i": i_,
"x_array": X_str,
"dim": coords_space.dim,
"xndof": coords_element.space_dimension(),
# FS will always either be a functionspace or
# vectorfunctionspace, so just accessing dim here is safe
# (we don't need to go through ufl_element.value_shape())
"nfdof": to_element.space_dimension() * np.prod(fs.dim, dtype=int),
"ndof": to_element.space_dimension(),
"assign_dim": np.prod(expression.value_shape(), dtype=int)
}
init = ast.FlatBlock("""
const double %(X)s[%(ndof)d][%(xndof)d] = %(x_array)s;
double %(x)s[%(dim)d];
const double pi = 3.141592653589793;
""" % vals)
block = ast.FlatBlock("""
for (unsigned int %(d)s=0; %(d)s < %(dim)d; %(d)s++) {
%(x)s[%(d)s] = 0;
for (unsigned int %(i)s=0; %(i)s < %(xndof)d; %(i)s++) {
%(x)s[%(d)s] += %(X)s[%(k)s][%(i)s] * %(x_)s[%(i)s][%(d)s];
};
};
""" % vals)
loop = ast.c_for(k, "%(ndof)d" % vals, ast.Block([block] + ass_exp,
open_scope=True))
user_args = []
user_init = []
for _, arg in expression._user_args:
if arg.shape == (1, ):
user_args.append(ast.Decl("double *", "%s_" % arg.name))
user_init.append(ast.FlatBlock("const double %s = *%s_;" %
(arg.name, arg.name)))
else:
user_args.append(ast.Decl("double *", arg.name))
kernel_code = ast.FunDecl("void", "expression_kernel",
[ast.Decl("double", ast.Symbol(A, (int("%(nfdof)d" % vals),))),
ast.Decl("double**", x_)] + user_args,
ast.Block(user_init + [init, loop],
open_scope=False))
return op2.Kernel(kernel_code, "expression_kernel")
def insert_features_from_path(dataset_path,
insert_dataset_path,
field_names=None,
**kwargs):
"""Insert features into dataset from another dataset.
Args:
dataset_path (str): Path of the dataset.
insert_dataset_path (str): Path of dataset to insert features from.
field_names (iter): Collection of field names to insert. Listed field must be
present in both datasets. If field_names is None, all fields will be
inserted.
**kwargs: Arbitrary keyword arguments. See below.
Keyword Args:
insert_where_sql (str): SQL where-clause for insert-dataset subselection.
use_edit_session (bool): Flag to perform updates in an edit session. Default is
False.
log_level (str): Level to log the function at. Defaults to 'info'.
Returns:
str: Path of the dataset updated.
"""
kwargs.setdefault('insert_where_sql')
kwargs.setdefault('use_edit_session', False)
log = leveled_logger(LOG, kwargs.get('log_level', 'info'))
log("Start: Insert features into %s from %s.", dataset_path,
insert_dataset_path)
meta = {
'dataset': dataset_metadata(dataset_path),
'insert': dataset_metadata(insert_dataset_path)
}
if field_names is None:
keys = set.intersection(*(set(
name.lower() for name in _meta['field_names_tokenized'])
for _meta in meta.values()))
else:
keys = set(name.lower() for name in contain(field_names))
# OIDs & area/length "fields" have no business being part of an update.
# Geometry itself is handled separately in append function.
for _meta in meta.values():
for key in chain(*_meta['field_token'].items()):
keys.discard(key)
append_kwargs = {
'inputs': unique_name('view'),
'target': dataset_path,
'schema_type': 'no_test',
'field_mapping': arcpy.FieldMappings()
}
# Create field maps.
# ArcGIS Pro's no-test append is case-sensitive (verified 1.0-1.1.1).
# Avoid this problem by using field mapping.
# BUG-000090970 - ArcGIS Pro 'No test' field mapping in Append tool does
# not auto-map to the same field name if naming convention differs.
for key in keys:
field_map = arcpy.FieldMap()
field_map.addInputField(insert_dataset_path, key)
append_kwargs['field_mapping'].addFieldMap(field_map)
view = DatasetView(
insert_dataset_path,
kwargs['insert_where_sql'],
view_name=append_kwargs['inputs'],
# Must be nonspatial to append to nonspatial table.
force_nonspatial=(not meta['dataset']['is_spatial']))
session = Editor(meta['dataset']['workspace_path'],
kwargs['use_edit_session'])
with view, session:
arcpy.management.Append(**append_kwargs)
feature_count = Counter({'inserted': view.count})
log("%s features inserted.", feature_count['inserted'])
log("End: Insert.")
return feature_count