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Add 'batch' option to set command
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@dominikl
dominikl committed Dec 2, 2019
1 parent 957bb12 commit 5d88206
Showing 1 changed file with 121 additions and 65 deletions.
186 changes: 121 additions & 65 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 concurrent.futures
import sys
import time
import json
Expand Down Expand Up @@ -397,6 +398,11 @@ def _configure(self, parser):
help="Local file or OriginalFile:ID which specifies the "
"rendering settings")

set_cmd.add_argument(
"--batch", type=int, default=1,
help="Batch size to process simultaneously"
)

test.add_argument(
"--force", action="store_true",
help="Force creation of pixel data file in binary "
Expand All @@ -415,7 +421,7 @@ def _lookup(self, gateway, type, oid):
self.ctx.die(110, "No such %s: %s" % (type, oid))
return obj

def render_images(self, gateway, object, batch=100):
def load_images(self, gateway, object, batch=100):
"""
Get the images.
Expand All @@ -430,12 +436,12 @@ def render_images(self, gateway, object, batch=100):

if isinstance(object, list):
for x in object:
for rv in self.render_images(gateway, x, batch):
for rv in self.load_images(gateway, x, batch):
yield rv
elif isinstance(object, Screen):
scr = self._lookup(gateway, "Screen", object.id)
for plate in scr.listChildren():
for rv in self.render_images(gateway, plate._obj, batch):
for rv in self.load_images(gateway, plate._obj, batch):
yield rv
elif isinstance(object, Plate):
plt = self._lookup(gateway, "Plate", object.id)
Expand All @@ -456,7 +462,7 @@ def render_images(self, gateway, object, batch=100):
elif isinstance(object, Project):
prj = self._lookup(gateway, "Project", object.id)
for ds in prj.listChildren():
for rv in self.render_images(gateway, ds._obj, batch):
for rv in self.load_images(gateway, ds._obj, batch):
yield rv

elif isinstance(object, Dataset):
Expand Down Expand Up @@ -486,7 +492,7 @@ def render_images(self, gateway, object, batch=100):
def info(self, args):
""" Implements the 'info' command """
first = True
for img in self.render_images(self.gateway, args.object, batch=1):
for img in self.load_images(self.gateway, args.object, batch=1):
ro = RenderObject(img)
if args.style == 'plain':
self.ctx.out(str(ro))
Expand All @@ -506,8 +512,8 @@ def info(self, args):
@gateway_required
def copy(self, args):
""" Implements the 'copy' command """
for src_img in self.render_images(self.gateway, args.object, batch=1):
for targets in self.render_images(self.gateway, args.target):
for src_img in self.load_images(self.gateway, args.object, batch=1):
for targets in self.load_images(self.gateway, args.target):
batch = dict()
for target in targets:
if target.id == src_img.id:
Expand All @@ -532,7 +538,7 @@ def copy(self, args):
self._generate_thumbs(list(batch.values()))

def update_channel_names(self, gateway, obj, namedict):
for targets in self.render_images(gateway, obj):
for targets in self.load_images(gateway, obj):
iids = [img.id for img in targets]
self._update_channel_names(self, iids, namedict)

Expand All @@ -550,13 +556,10 @@ def _generate_thumbs(self, images):
self.ctx.dbg("Image:%s got thumbnail in %2.2fs" % (
img.id, stop - start))

def _read_default_planes(self, img, data, ignore_errors=False):
def _read_default_planes(self, img, def_z=None, def_t=None,
ignore_errors=False):
"""Read and validate the default planes"""

# Read values from dictionary
def_z = data['z'] if 'z' in data else None
def_t = data['t'] if 't' in data else None

# Minimal validation: default planes should be 1-indexed integers
if (def_z is not None) and (def_z < 1 or int(def_z) != def_z):
self.ctx.die(
Expand Down Expand Up @@ -639,69 +642,122 @@ def _read_channels(self, data):
colourlist.append(c.color)
return (namedict, cindices, rangelist, colourlist)

def _set_rendering_settings(self, img, disable, def_z, def_t, cindices,
rangelist, colourlist, greyscale, skipthumbs,
ignore_errors):
"""
Set the rendering settings for an image
:param img: The image
:param disable: Flag if channels not in cindices should be disabled
:param def_z: The default z
:param def_t: The default t
:param cindices: The channel indices
:param rangelist: The window start end ranges
:param colourlist: The channel colors
:param greyscale: Flag if greyscale
:param skipthumbs: Flag to skip thumbnail generation
:param ignore_errors: Flag to ignore errors
:return: The image id
"""
(def_z, def_t) = self._read_default_planes(
img, def_z, def_t, ignore_errors=ignore_errors)

reactivatechannels = []

if not disable:
# Calling set_active_channels will disable channels which
# are not specified, have to keep track of them and
# re-activate them later again
imgchannels = img.getChannels()
for ci, ch in enumerate(imgchannels, 1):
if ci not in cindices and -ci not in cindices \
and ch.isActive():
reactivatechannels.append(ci)

img.set_active_channels(
cindices, windows=rangelist, colors=colourlist)

if greyscale is not None:
if greyscale:
img.setGreyscaleRenderingModel()
else:
img.setColorRenderingModel()

if len(reactivatechannels) > 0:
img.set_active_channels(reactivatechannels)

if def_z:
img.setDefaultZ(def_z - 1)
if def_t:
img.setDefaultT(def_t - 1)

try:
img.saveDefaults()
self.ctx.dbg(
"Updated rendering settings for Image:%s" % img.id)
if not skipthumbs:
self._generate_thumbs([img])
return img.id
except Exception as e:
self.ctx.err('ERROR: %s' % e)
if not ignore_errors:
self.ctx.die(141)
finally:
img._closeRE()

@gateway_required
def set(self, args):
""" Implements the 'set' command """
data = self._load_rendering_settings(
args.channels, session=self.client.getSession())

(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):
iids.append(img.id)

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

reactivatechannels = []
if not args.disable:
# Calling set_active_channels will disable channels which
# are not specified, have to keep track of them and
# re-activate them later again
imgchannels = img.getChannels()
for ci, ch in enumerate(imgchannels, 1):
if ci not in cindices and -ci not in cindices\
and ch.isActive():
reactivatechannels.append(ci)

img.set_active_channels(
cindices, windows=rangelist, colors=colourlist)

if greyscale is not None:
if greyscale:
img.setGreyscaleRenderingModel()
else:
img.setColorRenderingModel()

if len(reactivatechannels) > 0:
img.set_active_channels(reactivatechannels)

if def_z:
img.setDefaultZ(def_z - 1)
if def_t:
img.setDefaultT(def_t - 1)

try:
img.saveDefaults()
self.ctx.dbg(
"Updated rendering settings for Image:%s" % img.id)
if not args.skipthumbs:
self._generate_thumbs([img])
except Exception as e:
self.ctx.err('ERROR: %s' % e)
finally:
img._closeRE()

if not iids:
self.ctx.die(113, "ERROR: No images found for %s %d" %
(args.object.__class__.__name__, args.object.id._val))
def_z = data['z'] if 'z' in data else None
def_t = data['t'] if 't' in data else None

if namedict:
self._update_channel_names(self.gateway, iids, namedict)
# Turn off cache usage in order to make this work in parallel
self.gateway.cacheServices(False)

for img_batch in self.load_images(self.gateway, args.object,
batch=args.batch):
if not isinstance(img_batch, list):
img_batch = [img_batch]

with concurrent.futures.ThreadPoolExecutor() as executor:
future_image = {executor.submit(self._set_rendering_settings,
img, args.disable, def_z, def_t,
cindices, rangelist, colourlist,
greyscale, args.skipthumbs,
args.ignore_errors):
img for img in img_batch }

for future in concurrent.futures.as_completed(future_image):
img = future_image[future]
try:
future.result()
except Exception as exc:
self.ctx.err('ERROR: Image %d: %s' % (img.id, exc))
if not args.ignore_errors:
self.ctx.die(142)

if namedict:
try:
batch_iids = [img.id for img in img_batch]
self._update_channel_names(self.gateway, batch_iids,
namedict)
except Exception as exc:
self.ctx.err('ERROR: Could not set channel name:%s'
% exc)
if not args.ignore_errors:
self.ctx.die(143)

self.gateway.cacheServices(True)

def edit(self, args):
self.ctx.die(112, "ERROR: 'edit' command has been renamed to 'set'")
Expand All @@ -710,7 +766,7 @@ def edit(self, args):
def test(self, args):
""" Implements the 'test' command """
self.gateway.SERVICE_OPTS.setOmeroGroup('-1')
for img in self.render_images(self.gateway, args.object, batch=1):
for img in self.load_images(self.gateway, args.object, batch=1):
self.test_per_pixel(
self.client, img.getPrimaryPixels().id, args.force, args.thumb)

Expand Down

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