class KilosortHelperParameters(DefaultSchema):
kilosort_version = Int(required=True,
default=2,
help='Kilosort version to use (1, 2, or 3)')
surface_channel_buffer = Int(
required=False,
default=15,
help=
'Number of channels above brain surface to include in spike sorting')
matlab_home_directory = InputDir(
help='Location from which Matlab files can be copied and run.')
kilosort_repository = InputDir(
help='Local directory for the Kilosort source code repository.')
kilosort_params = Nested(
KilosortParameters,
required=False,
help='Parameters used to auto-generate a Kilosort config file')
kilosort2_params = Nested(
Kilosort2Parameters,
required=False,
help='Parameters used to auto-generate a Kilosort2 config file')
kilosort3_params = Nested(
Kilosort3Parameters,
required=False,
help='Parameters used to auto-generate a Kilosort3 config file')
class MontageSolverSchema(ArgSchema):
data_dir = InputDir(
required=False,
description="directory containing metafile, images, and matches")
metafile = InputFile(
required=False,
description=("fullpath to metafile. Helps in the case of multiple"
" metafiles in one directory. data_dir will take "
" os.path.dirname(metafile)"))
output_dir = OutputDir(required=False,
missing=None,
default=None,
description="directory for output files")
read_transform_from = Str(
required=False,
missing='metafile',
default='metafile',
validator=mm.validate.OneOf(['metafile', 'reffile', 'dict']),
description="3 possible ways to read in the reference transform")
ref_transform = InputFile(required=False,
missing=None,
default=None,
description="transform json")
ref_transform_dict = Dict(require=False,
missing=None,
description="transform in from memory")
ransacReprojThreshold = Float(
required=False,
missing=10.0,
default=10.0,
description=("passed into cv2.estimateAffinePartial2D()"
"for RANSAC filtering of montage template matches"))
compress_output = Boolean(
required=False,
missing=True,
default=True,
description=("tilespecs will be .json or .json.gz"))
solver_templates = List(
Str,
required=True,
description="input json basenames for the solver args")
solver_template_dir = InputDir(
required=True, description="location of the templates for the solver")
@mm.post_load
def check_solver_inputs(self, data):
for args in data['solver_templates']:
argpath = os.path.join(data['solver_template_dir'], args)
if not os.path.isfile(argpath):
raise mm.ValidationError("solver arg file doesn't exist: %s" %
argpath)
@mm.post_load
def check_metafile(self, data):
if ('data_dir' not in data) & ('metafile' not in data):
raise mm.ValidationError(" must specify either data_dir"
" or metafile")
class Directories(DefaultSchema):
ecephys_directory = InputDir(
help=
'Location of the ecephys_spike_sorting directory containing modules directory'
)
npx_directory = InputDir(help='Location of raw neuropixels binary files')
kilosort_output_directory = OutputDir(
help='Location of Kilosort output files')
extracted_data_directory = OutputDir(
help='Location for NPX/CatGT processed files')
kilosort_output_tmp = OutputDir(help='Location for temporary KS output')
class KilosortHelperParameters(DefaultSchema):
kilosort_version = Int(required=True, default=2, help='Kilosort version to use (1 or 2)')
spikeGLX_data = Bool(required=True, default=False, help='If true, use SpikeGLX metafile to build chanMap')
ks_make_copy = Bool(required=False, default=False, help='If true, make a copy of the original KS output')
surface_channel_buffer = Int(required=False, default=15, help='Number of channels above brain surface to include in spike sorting')
matlab_home_directory = InputDir(help='Location from which Matlab files can be copied and run.')
kilosort_repository = InputDir(help='Local directory for the Kilosort source code repository.')
npy_matlab_repository = InputDir(help='Local directory for the npy_matlab repo for writing phy output')
kilosort_params = Nested(KilosortParameters, required=False, help='Parameters used to auto-generate a Kilosort config file')
kilosort2_params = Nested(Kilosort2Parameters, required=False, help='Parameters used to auto-generate a Kilosort2 config file')
class CatGTParams(DefaultSchema):
run_name = String(required=True,
help='undecorated run name (no g or t indices')
gate_string = String(required=True, default='0', help='gate string')
trigger_string = String(
required=True,
default='0,0',
help='string specifying trials to concatenate, e.g. 0,200')
probe_string = String(required=True,
default='0',
help='string specifying probes, e.g. 0:3')
stream_string = String(required=True,
default='-ap',
help='string specifying which streams to process')
car_mode = String(
required=False,
default='None',
help='Comaon average reference mode. Must = None, gbldmx, or loccar ')
loccar_inner = Int(required=False,
default=2,
help='Inner radius for loccar in sites')
loccar_outer = Int(required=False,
default=8,
help='Outer radius for loccar in sites')
cmdStr = String(
required=True,
default='-prbfld -aphipass=300 -gbldmx -gfix=0.40,0.10,0.02',
help='input stream filter, error correct and extract settings for CatGT'
)
extract_string = String(required=True,
default='',
help='extract edges from datastreams')
catGTPath = InputDir(help='directory containing the CatGT executable.')
class UploadTileSpecParameters(RenderParameters):
inputDir = InputDir(
required=True,
metadata={'description': 'input directory of tilespecs'})
outputStack = Str(
required=True,
metadata={'description': 'name of output stack to upload to render'})
class CreateFastStacksParameters(RenderParameters):
projectDirectory = InputDir(required=True,
description='path to project root')
pool_size = Int(require=False,default=20,
description='number of parallel threads to use')
delete_stack = Boolean(require=False,default=True,
description='flag to decide whether stack should be deleted before new upload')
class MipMapDirectories(DefaultSchema):
level = Int(
required=True,
description=("mipMapLevel for which parent directory will be changed"))
directory = InputDir(
required=True,
description=("directory where relocated mipmaps are found."))
class tPrimeParams(DefaultSchema):
tPrime_path = InputDir(help='directory containing the TPrime executable.')
sync_period = Float(default=1.0, help='Period of sync waveform (sec).')
toStream_sync_params = String(
required=False,
default='SY=0,384,6,500',
help=
'string of CatGT params used to extract to stream sync edges, e.g. SY=0,384,6,500'
)
ni_sync_params = String(
required=False,
default='XA=0,1,3,500',
help=
'string of CatGT params used to extract NI sync edges, e.g. XA=0,1,3,500'
)
ni_ex_list = String(
required=False,
default='',
help=
'string of CatGT params used to extract edges from ni, e.g. XA=0,1,3,500'
)
im_ex_list = String(
required=False,
default='',
help=
'string of CatGT params used to extract edges from im streams, e.g. SY=0,384,6,500'
)
tPrime_3A = Boolean(required=False, default=False, help='is this 3A data?')
toStream_path_3A = String(required=False,
help='full path to toStream edges file')
fromStream_list_3A = List(
String,
required=False,
help='list of full paths to fromStream edges files')
class PointMatchClientParametersQsub(
RenderParameters, SIFTPointMatchParameters, SparkOptions):
sparkhome = InputDir(
required=False,
default="/allen/aibs/pipeline/image_processing/"
"volume_assembly/utils/spark",
missing="/allen/aibs/pipeline/image_processing/"
"volume_assembly/utils/spark",
description="Path to the spark home directory")
pbs_template = InputFile(
required=True,
description="pbs template to wrap spark job")
no_nodes = Int(
required=False,
default=30,
missing=10,
description='Number of nodes to run the pbs job')
ppn = Int(
required=False,
default=30,
missing=30,
description='Number of processors per node (default = 30)')
queue_name = Str(
required=False,
default='connectome',
missing='connectome',
description='Name of the queue to submit the job')
logdir = OutputDir(
required=True,
description="location to set logging for qsub command"
)
class BaseStackParameters(DefaultSchema):
stack = Str(required=True, description="Stack name")
owner = Str(
required=False,
default=None,
missing=None,
description="Owner of the stack (defaults to render clients' owner)")
project = Str(required=False,
default=None,
missing=None,
description="Project of the stack")
service_host = Str(
required=False,
default=None,
missing=None,
description="url of render service host (without http://)")
baseURL = Str(required=False,
default=None,
missing=None,
description="Base Render URL")
renderbinPath = InputDir(required=False,
default=None,
missing=None,
description="Path to render's client scripts")
verbose = Int(required=False,
default=0,
missing=0,
description="Verbose output from solver needed?")
class GenerateEMTileSpecsParameters(ArgSchema):
metafile = InputFile(
required=True,
description="metadata file containing TEMCA acquisition data")
maskUrl = InputFile(required=False,
default=None,
missing=None,
description="absolute path to image mask to apply")
image_directory = InputDir(
required=False,
description=("directory used in determining absolute paths to images. "
"Defaults to parent directory containing metafile "
"if omitted."))
maximum_intensity = Int(
required=False,
default=255,
description=("intensity value to interpret as white"))
minimum_intensity = Int(
required=False,
default=0,
description=("intensity value to interpret as black"))
z = Float(required=False, default=0, description=("z value"))
sectionId = Str(
required=False,
description=("sectionId to apply to tiles during ingest. "
"If unspecified will default to a string "
"representation of the float value of z_index."))
output_path = OutputFile(required=False,
description="directory for output files")
compress_output = Boolean(
required=False,
missing=True,
default=True,
escription=("tilespecs will be .json or .json.gz"))
class RenderSectionAtScaleOutput(argschema.schemas.DefaultSchema):
image_directory = InputDir(
required=True,
description=('Directory in which the downsampled '
'section images are saved'))
temp_stack = Str(required=True,
description=('The temp stack that was used to '
'generate the downsampled sections'))
class GenerateEMTileSpecsParameters(OutputStackParameters):
metafile = InputFile(
required=False,
description="metadata file containing TEMCA acquisition data")
metafile_uri = Str(
required=True,
description=("uri of metadata containing TEMCA acquisition data"))
# FIXME maskUrl and image_directory are not required -- posix_to_uri should support this
maskUrl = InputFile(required=False,
default=None,
missing=None,
description="absolute path to image mask to apply")
maskUrl_uri = Str(required=False,
default=None,
missing=None,
description=("uri of image mask to apply"))
image_directory = InputDir(
required=False,
description=("directory used in determining absolute paths to images. "
"Defaults to parent directory containing metafile "
"if omitted."))
image_prefix = Str(
required=False,
description=(
"prefix used in determining full uris of images in metadata. "
"Defaults to using the / delimited prefix to "
"the metadata_uri if omitted"))
maximum_intensity = Int(
required=False,
default=255,
description=("intensity value to interpret as white"))
minimum_intensity = Int(
required=False,
default=0,
description=("intensity value to interpret as black"))
sectionId = Str(
required=False,
description=("sectionId to apply to tiles during ingest. "
"If unspecified will default to a string "
"representation of the float value of z_index."))
@pre_load
def metafile_to_uri(self, data):
rendermodules.utilities.schema_utils.posix_to_uri(
data, "metafile", "metafile_uri")
# FIXME not required -- does this work
@pre_load
def maskUrl_to_uri(self, data):
rendermodules.utilities.schema_utils.posix_to_uri(
data, "storage_directory", "storage_prefix")
@pre_load
def image_directory_to_prefix(self, data):
rendermodules.utilities.schema_utils.posix_to_uri(
data, "image_directory", "image_prefix")
class DetectMontageDefectsParameters(RenderParameters, ZValueParameters,
ProcessPoolParameters):
prestitched_stack = Str(required=True,
description='Pre stitched stack (raw stack)')
poststitched_stack = Str(required=True,
description='Stitched montage stack')
match_collection = Str(
reuqired=True,
description='Name of the montage point match collection')
match_collection_owner = Str(
required=False,
default=None,
missing=None,
description='Name of the match collection owner')
residual_threshold = Int(
required=False,
default=4,
missing=4,
description=('threshold value to filter residuals '
'for detecting seams (default = 4)'))
neighbors_distance = Int(
required=False,
default=80,
missing=80,
description=('distance in pixels to look for '
'neighboring points in seam detection (default = 60)'))
min_cluster_size = Int(
required=False,
default=12,
missing=12,
description=(
'minimum number of point matches required in each cluster '
'for taking it into account for seam detection (default = 7)'))
threshold_cutoff = argschema.fields.List(
argschema.fields.Float,
required=False,
default=[0.005, 0.005],
description='Threshold for MAD cutoff in x and y')
plot_sections = Bool(
required=False,
default=True,
missing=True,
description=("Do you want to plot the sections with defects "
"(holes or gaps)?. Will plot Bokeh plots in a html file"))
out_html_dir = InputDir(
required=False,
default=None,
missing=None,
description="Folder to save the Bokeh plot defaults to /tmp directory")
@post_load
def add_match_collection_owner(self, data):
if data['match_collection_owner'] is None:
data['match_collection_owner'] = data['render']['owner']
class UploadTileDirParameters(RenderParameters):
inputTileDirectory = InputDir(required=True,
description='path to project root')
tilespecDirectory = Str(required=True,
description='path to project root')
outputStack = Str(required=True,
description='Output stack')
pool_size = Int(require=False,default=20,
description='number of parallel threads to use')
delete_stack = Boolean(require=False,default=True,
description='flag to decide whether stack should be deleted before new upload')
class GenerateSBEMTileSpecsParameters(OutputStackParameters):
image_directory = InputDir(
required=True,
description=("directory used in determining absolute paths to images. "
"Defaults to parent directory containing metafile "
"if omitted."))
image_prefix = Str(
required=False,
description=(
"prefix used in determining full uris of images in metadata. "
"Defaults to using the / delimited prefix to "
"the metadata_uri if omitted"))
class TileSetIngestSchema(argschema.ArgSchema):
storage_directory = InputDir(
required=False, description=(
"Directory which stores acquisition data. "
"Non-file uris must use storage_prefix"))
storage_prefix = Str(required=True, description=(
"uri prefix for acquisition data."))
section = Nested(Section, required=False,
description="")
acquisition_data = Nested(AcquisitionData, required=False)
# TODO test this
@marshmallow.pre_load
def directory_to_storage_prefix(self, data):
asap.utilities.schema_utils.posix_to_uri(
data, "storage_directory", "storage_prefix")
class CreateFastStacksParameters(RenderParameters):
statetableFile = InputFile(required=True, description='state table file')
projectDirectory = InputDir(required=True,
description='path to project root')
outputStackPrefix = Str(
required=False,
default="ACQ",
description=
'prefix to include in front of channel name for render stack')
pool_size = Int(require=False,
default=20,
description='number of parallel threads to use')
delete_stack = Boolean(
require=False,
default=True,
description=
'flag to decide whether stack should be deleted before new upload')
class SparkOptions(argschema.schemas.DefaultSchema):
jarfile = Str(required=True, description=(
"spark jar to call java spark command"))
className = Str(required=True, description=(
"spark class to call"))
driverMemory = Str(required=False, default='6g', description=(
"spark driver memory (important for local spark)"))
memory = Str(
required=False,
description="Memory required for spark job")
sparkhome = InputDir(required=True, description=(
"Spark home directory containing bin/spark_submit"))
spark_files = List(InputFile, required=False, description=(
"list of spark files to add to the spark submit command"))
spark_conf = Dict(required=False, description=(
"dictionary of key value pairs to add to spark_submit "
"as --conf key=value"))
class CatGTParams(DefaultSchema):
run_name = String(required=True,
help='undecorated run name (no g or t indices')
gate_string = String(required=True, default='0', help='gate string')
trigger_string = String(
required=True,
default='0,0',
help='string specifying trials to concatenate, e.g. 0,200')
probe_string = String(required=True,
default='0',
help='string specifying probes, e.g. 0:3')
stream_string = String(required=True,
default='-ap',
help='string specifying which streams to process')
cmdStr = String(
required=True,
default='-prbfld -aphipass=300 -gbldmx -gfix=0.40,0.10,0.02',
help='input stream filter, error correct settings for CatGT')
catGTPath = InputDir(help='directory containing the CatGT executable.')
class ViewMatchesSchema(ArgSchema):
collection_path = InputFile(
required=False,
description="if specified, will read collection from here")
collection_basename = Str(
required=True,
missing="collection.json",
default="collection.json",
description=("basename for collection file if collection_path"
" not specified. will also check for .json.gz"))
data_dir = InputDir(
required=True,
description=("directory containing image files. Will also be dir"
" dir for collection path, if not otherwise specified"))
resolved_tiles = List(
Str,
required=True,
missing=["resolvedtiles.json.gz", "resolvedtiles_input.json.gz"],
description=("will take the transform from the first file"
" matching this list, if possible"))
transform_file = InputFile(
required=False,
description=("if provided, will get lens correction transform "
" from here"))
view_all = Boolean(
required=True,
missing=False,
default=False,
description=("will plot all the pair matches. can be useful "
"for lens correction to file. probably not desirable "
"for montage"))
show = Boolean(required=True,
missing=True,
default=True,
description=("show on screen?"))
match_index = Int(required=True,
missing=0,
default=0,
description=("which index of self.matches to plot"))
pdf_out = OutputFile(required=True,
missing='./view_matches_output.pdf',
default='./view_matches_output.pdf',
description="where to write the pdf output")
class AddMipMapsToStackParameters(StackTransitionParameters):
mipmap_dir = InputDir(
required=False,
description='directory to which the mipmaps will be stored')
mipmap_prefix = Str(
required=True,
description=("uri prefix from which mipmap locations are built."))
levels = mm.fields.Int(
required=False,
default=6,
description='number of levels of mipmaps, default is 6')
imgformat = mm.fields.Str(
required=False,
default="tiff",
description='mipmap image format, default is tiff')
@pre_load
def mipmap_directory_to_prefix(self, data):
asap.utilities.schema_utils.posix_to_uri(data, "mipmap_dir",
"mipmap_prefix")
class CreateSectionPolygonsParameters(RenderParameters):
stack = Str(
required=True,
description=
'stack sectionImages are based upon (assumes section bounds for images)'
)
sectionImageDir = InputDir(
required=True,
description=
'stack sectionImages directory (assumes section bounds for images)')
polygon_dir = Str(
required=True,
description='directory to save json seciton boundaries into')
isHorizontal = Boolean(
required=True,
description=
'flag as to whether the sections are vertically or horizontally oriented'
)
class MeanWaveformParams(DefaultSchema):
samples_per_spike = Int(required=True,
default=82,
help='Number of samples to extract for each spike')
pre_samples = Int(
required=True,
default=20,
help='Number of samples between start of spike and the peak')
num_epochs = Int(required=True,
default=1,
help='Number of epochs to compute mean waveforms')
spikes_per_epoch = Int(require=True,
default=100,
help='Max number of spikes per epoch')
upsampling_factor = Float(
require=False,
default=200 / 82,
help='Upsampling factor for calculating waveform metrics')
spread_threshold = Float(
require=False,
default=0.12,
help='Threshold for computing channel spread of 2D waveform')
site_range = Int(require=False,
default=16,
help='Number of sites to use for 2D waveform metrics')
cWaves_path = InputDir(require=False,
help='directory containing the TPrime executable.')
use_C_Waves = Bool(require=False,
default=False,
help='Use faster C routine to calculate mean waveforms')
snr_radius = Int(
require=False,
default=8,
help='disk radius (chans) about pk-chan for snr calculation in C_waves'
)
mean_waveforms_file = String(required=True,
help='Path to mean waveforms file (.npy)')
class LensCorrectionSchema(ArgSchema):
data_dir = InputDir(
required=True,
description="directory containing metafile, images, and matches")
output_dir = OutputDir(required=False,
description="directory for output files")
mask_file = InputFile(required=False,
default=None,
missing=None,
description="mask to apply to each tile")
nvertex = Int(required=False,
default=1000,
missinf=1000,
description="maximum number of vertices to attempt")
ransac_thresh = Float(required=False,
default=5.0,
missing=5.0,
description="ransac outlier threshold")
regularization = Nested(regularization, missing={})
good_solve = Nested(good_solve_criteria, missing={})
ignore_match_indices = List(
Int,
required=False,
default=None,
missing=None,
description=("debug feature for ignoring certain indices"
" of the match collection"))
compress_output = Boolean(
required=False,
missing=True,
default=True,
description=("tilespecs will be .json or .json.gz"))
timestamp = Boolean(required=False,
missing=False,
default=False,
description="add a timestamp to basename output")
class SolverParameters(DefaultSchema):
# NOTE: Khaled's EM_aligner needs some of the boolean variables as Integers
# Hence providing the input as Integers
degree = Int(required=True,
default=1,
description="Degree of transformation 1 - affine, "
"2 - second order polynomial, maximum is 3")
solver = Str(required=False,
default='backslash',
missing='backslash',
description="Solver type - default is backslash")
transfac = Float(required=False,
default=1e-15,
missing=1e-15,
description='Translational factor')
lambda_value = Float(required=True, description="regularization parameter")
edge_lambda = Float(required=True,
description="edge lambda regularization parameter")
nbrs = Int(required=False,
default=3,
missing=3,
description="No. of neighbors")
nbrs_step = Int(required=False,
default=1,
missing=1,
description="Step value to increment the # of neighbors")
xs_weight = Float(
required=True,
description="Weight ratio for cross section point matches")
min_points = Int(
required=True,
default=8,
description="Minimum no. of point matches per tile pair defaults to 8")
max_points = Int(required=True,
default=100,
description="Maximum no. of point matches")
filter_point_matches = Int(
required=False,
default=1,
missing=1,
description='set to a value 1 if point matches must be filtered')
outlier_lambda = Float(
required=True,
default=100,
description="Outlier lambda - large numbers result in "
"fewer tiles excluded")
min_tiles = Int(required=False,
default=2,
missing=2,
description="minimum number of tiles")
Width = Int(required=False,
default=3840,
missing=3840,
description='Width of the tiles (default = 3840)')
Height = Int(required=False,
default=3840,
missing=3840,
description='Height of the tiles (default= 3840)')
outside_group = Int(required=False,
default=0,
missing=0,
description='Outside group parameter (default = 0)')
matrix_only = Int(required=False,
default=0,
missing=0,
description="0 - solve (default), 1 - only generate "
"the matrix. For debugging only")
distribute_A = Int(required=False,
default=1,
missing=1,
description="Shards of A matrix")
dir_scratch = InputDir(required=True, description="Scratch directory")
distributed = Int(required=False,
default=0,
missing=0,
description="distributed or not?")
disableValidation = Int(
required=False,
default=1,
missing=1,
description="Disable validation while ingesting tiles?")
use_peg = Int(required=False,
default=0,
missing=0,
description="use pegs or not")
complete = Int(required=False,
default=0,
missing=0,
description="Set stack state to complete after processing?")
verbose = Int(required=False,
default=0,
missing=0,
description="want verbose output?")
debug = Int(required=False,
default=0,
missing=0,
description="Debug mode?")
constrain_by_z = Int(required=False,
default=0,
missing=0,
description='Contrain by z')
sandwich = Int(required=False,
default=0,
missing=0,
description='Sandwich parameter for solver')
constraint_fac = Float(required=False,
default=1e+15,
missing=1e+15,
description='Constraint factor')
pmopts = Nested(PointMatchParameters,
required=True,
description='Point match filtering parameters')
pastix = Nested(PastixParameters,
required=False,
default=None,
missing=None,
description="Pastix parameters if solving using Pastix")
class BasicInputDir(ArgSchema):
input_dir = InputDir(required=True,
metadata={'description': 'a simple file'})
class MaterializeSectionsOutput(argschema.schemas.DefaultSchema):
zValues = List(Int, required=True)
rootDirectory = InputDir(required=True)
materializedDirectory = InputDir(required=True)
class BasicInputDir(ArgSchema):
input_dir = InputDir(required=True, description='a simple file')