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Add batchset for rendering a folder of datasets #50

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Add batchset for rendering a folder of datasets #50

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76 changes: 69 additions & 7 deletions src/omero_cli_render.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
from builtins import str
from builtins import range
from builtins import object
import os
import sys
import time
import json
Expand Down Expand Up @@ -123,6 +124,27 @@
# name (label) is still taken into account.
"""

BATCHSET_HELP = """Set rendering settings from a hierachy of rendering
definitions corresponding to an OMERO container hierarchy

Only Datasets in a single Project are currently supported.
The Project must be passed as Project:<id>

Example rendering definition tree:
/renderdefs
/dataset1
# this will be applied to a dataset called "dataset1" in Project:<id>
/renderdef.yml
/dataset2
# this will be applied to a dataset called "dataset2" in Project:<id>
/renderdef.yml

omero render batchset Project:<id> /renderdefs

The rendering definitions must be in a file called renderdef.yml
See the set command for the specification of these files.
"""

TEST_HELP = """Test that underlying pixel data is available

The syntax for specifying objects is: <object>:<id>
Expand Down Expand Up @@ -361,6 +383,7 @@ def _configure(self, parser):
info = parser.add(sub, self.info, INFO_HELP)
copy = parser.add(sub, self.copy, COPY_HELP)
set_cmd = parser.add(sub, self.set, SET_HELP)
batchset = parser.add(sub, self.batchset, BATCHSET_HELP)
edit = parser.add(sub, self.edit, EDIT_HELP)
test = parser.add(sub, self.test, TEST_HELP)

Expand All @@ -375,7 +398,13 @@ def _configure(self, parser):
x.add_argument("object", type=render_type, help=tgt_help,
nargs="+")

for x in (copy, set_cmd, edit):
batchset.add_argument("object", type=render_type, help=(
"Parent object containing the objects the rendering settings "
"apply to"))
batchset.add_argument("path", help=(
"Directory containing subdirectories with renderdefs."))

for x in (copy, set_cmd, edit, batchset):
x.add_argument(
"--skipthumbs", help="Do not regenerate thumbnails "
"immediately", action="store_true")
Expand All @@ -389,13 +418,14 @@ def _configure(self, parser):
copy.add_argument("target", type=render_type, help=tgt_help,
nargs="+")

for x in (set_cmd, edit):
for x in (set_cmd, edit, batchset):
x.add_argument(
"--disable", help="Disable non specified channels ",
action="store_true")
x.add_argument(
"--ignore-errors", help="Do not error on mismatching"
" rendering settings", action="store_true")
for x in (set_cmd, edit):
x.add_argument(
"channels",
help="Local file or OriginalFile:ID which specifies the "
Expand Down Expand Up @@ -653,21 +683,53 @@ def set(self, args):
""" Implements the 'set' command """
data = self._load_rendering_settings(
args.channels, session=self.client.getSession())
self._set(data, args.object,
args.ignore_errors, args.disable, args.skipthumbs)

@gateway_required
def batchset(self, args):
""" Implements the 'batchset' command """
if isinstance(args.object, Project):
project = self._lookup(self.gateway, 'Project', args.object.id)
datasets = dict((ch.name, ch) for ch in project.listChildren())
for d in os.listdir(args.path):
dpath = os.path.join(args.path, d)
if not os.path.isdir(dpath):
self.ctx.err('WARNING: "{}/{}" is not a directory'.format(
args.path, d))
continue
if d not in datasets:
self.ctx.die(101, 'ERROR: "{}" is not a dataset'.format(d))
for f in os.listdir(dpath):
fpath = os.path.join(dpath, f)
if f != 'renderdef.yml':
self.ctx.err('WARNING: Ignoring file "{}/{}"'.format(
fpath))
continue
data = self._load_rendering_settings(
fpath, session=self.client.getSession())
self.ctx.out('Applying settings to {}'.format(d))
self._set(
data, datasets[d]._obj,
args.ignore_errors, args.disable, args.skipthumbs)

def _set(self, data, target, ignore_errors, disable, skipthumbs):
""" Utility method to apply rendering settings """
(namedict, cindices, rangelist, colourlist) = self._read_channels(
data)
greyscale = data.get('greyscale', None)
if greyscale is not None:
self.ctx.dbg('greyscale=%s' % greyscale)

iids = []
for img in self.render_images(self.gateway, args.object, batch=1):
for img in self.render_images(self.gateway, target, batch=1):
iids.append(img.id)

(def_z, def_t) = self._read_default_planes(
img, data, ignore_errors=args.ignore_errors)
img, data, ignore_errors=ignore_errors)

active_channels = []
if not args.disable:
if not disable:
# Calling set_active_channels will disable channels which
# are not specified.
# Need to reset ALL active channels after set_active_channels()
Expand Down Expand Up @@ -700,7 +762,7 @@ def set(self, args):
img.saveDefaults()
self.ctx.dbg(
"Updated rendering settings for Image:%s" % img.id)
if not args.skipthumbs:
if not skipthumbs:
self._generate_thumbs([img])
except Exception as e:
self.ctx.err('ERROR: %s' % e)
Expand All @@ -709,7 +771,7 @@ def set(self, args):

if not iids:
self.ctx.die(113, "ERROR: No images found for %s %d" %
(args.object.__class__.__name__, args.object.id._val))
(target.__class__.__name__, target.id._val))

if namedict:
self._update_channel_names(self.gateway, iids, namedict)
Expand Down