Geo obj to view скачать
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Geo obj to view скачать

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getGEO : Get a GEO object from NCBI or file

This function is the main user-level function in the GEOquery package. It directs the download (if no filename is specified) and parsing of a GEO SOFT format file into an R data structure specifically designed to make access to each of the important parts of the GEO SOFT format easily accessible.

Usage

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getGEO(GEO = NULL, filename = NULL, destdir = tempdir(), GSElimits = NULL, GSEMatrix = TRUE, AnnotGPL = FALSE, getGPL = TRUE, parseCharacteristics = TRUE) 

Arguments

A character string representing a GEO object for download and parsing. (eg., ‘GDS505′,’GSE2′,’GSM2′,’GPL96’)

The filename of a previously downloaded GEO SOFT format file or its gzipped representation (in which case the filename must end in .gz). Either one of GEO or filename may be specified, not both. GEO series matrix files are also handled. Note that since a single file is being parsed, the return value is not a list of esets, but a single eset when GSE matrix files are parsed.

The destination directory for any downloads. Defaults to the architecture-dependent tempdir. You may want to specify a different directory if you want to save the file for later use. Doing so is a good idea if you have a slow connection, as some of the GEO files are HUGE!

This argument can be used to load only a contiguous subset of the GSMs from a GSE. It should be specified as a vector of length 2 specifying the start and end (inclusive) GSMs to load. This could be useful for splitting up large GSEs into more manageable parts, for example.

A boolean telling GEOquery whether or not to use GSE Series Matrix files from GEO. The parsing of these files can be many orders-of-magnitude faster than parsing the GSE SOFT format files. Defaults to TRUE, meaning that the SOFT format parsing will not occur; set to FALSE if you for some reason need other columns from the GSE records.

A boolean defaulting to FALSE as to whether or not to use the Annotation GPL information. These files are nice to use because they contain up-to-date information remapped from Entrez Gene on a regular basis. However, they do not exist for all GPLs; in general, they are only available for GPLs referenced by a GDS

A boolean defaulting to TRUE as to whether or not to download and include GPL information when getting a GSEMatrix file. You may want to set this to FALSE if you know that you are going to annotate your featureData using Bioconductor tools rather than relying on information provided through NCBI GEO. Download times can also be greatly reduced by specifying FALSE.

A boolean defaulting to TRUE as to whether or not to parse the characteristics information (if available) for a GSE Matrix file. Set this to FALSE if you experience trouble while parsing the characteristics.

Details

getGEO functions to download and parse information available from NCBI GEO (http://www.ncbi.nlm.nih.gov/geo). Here are some details about what is avaible from GEO. All entity types are handled by getGEO and essentially any information in the GEO SOFT format is reflected in the resulting data structure.

From the GEO website:

The Gene Expression Omnibus (GEO) from NCBI serves as a public repository for a wide range of high-throughput experimental data. These data include single and dual channel microarray-based experiments measuring mRNA, genomic DNA, and protein abundance, as well as non-array techniques such as serial analysis of gene expression (SAGE), and mass spectrometry proteomic data. At the most basic level of organization of GEO, there are three entity types that may be supplied by users: Platforms, Samples, and Series. Additionally, there is a curated entity called a GEO dataset.

A Platform record describes the list of elements on the array (e.g., cDNAs, oligonucleotide probesets, ORFs, antibodies) or the list of elements that may be detected and quantified in that experiment (e.g., SAGE tags, peptides). Each Platform record is assigned a unique and stable GEO accession number (GPLxxx). A Platform may reference many Samples that have been submitted by multiple submitters.

A Sample record describes the conditions under which an individual Sample was handled, the manipulations it underwent, and the abundance measurement of each element derived from it. Each Sample record is assigned a unique and stable GEO accession number (GSMxxx). A Sample entity must reference only one Platform and may be included in multiple Series.

A Series record defines a set of related Samples considered to be part of a group, how the Samples are related, and if and how they are ordered. A Series provides a focal point and description of the experiment as a whole. Series records may also contain tables describing extracted data, summary conclusions, or analyses. Each Series record is assigned a unique and stable GEO accession number (GSExxx).

GEO DataSets (GDSxxx) are curated sets of GEO Sample data. A GDS record represents a collection of biologically and statistically comparable GEO Samples and forms the basis of GEO’s suite of data display and analysis tools. Samples within a GDS refer to the same Platform, that is, they share a common set of probe elements. Value measurements for each Sample within a GDS are assumed to be calculated in an equivalent manner, that is, considerations such as background processing and normalization are consistent across the dataset. Information reflecting experimental design is provided through GDS subsets.

Value

An object of the appropriate class (GDS, GPL, GSM, or GSE) is returned. If the GSEMatrix option is used, then a list of ExpressionSet objects is returned, one for each SeriesMatrix file associated with the GSE accesion. If the filename argument is used in combination with a GSEMatrix file, then the return value is a single ExpressionSet.

Warning

Some of the files that are downloaded, particularly those associated with GSE entries from GEO are absolutely ENORMOUS and parsing them can take quite some time and memory. So, particularly when working with large GSE entries, expect that you may need a good chunk of memory and that coffee may be involved when parsing.

Geo obj to view скачать

Understanding numbers, their relationships and numerical reasoning

Using symbols to solve equations and express patterns

Studying shapes, sizes and spatial relationships in mathematics

Quantifying and comparing attributes like length, weight and volume

Performing mathematical operations like addition, subtraction, division

Probability and Statistics

Analyzing uncertainty and likelihood of events and outcomes

OBJ GEO PLY to .vrmesh converter

This page describes the ply2vrmesh command-line utility.

Overview

The ply2vrmesh command-line utility can convert .ply, .obj, .bin, .geo, .bgeo, .hclassic, .bhclassic, .abc, and .vrscene files to .vrmesh files for rendering with V-Ray through V-Ray Proxy Objects .

Installation

Windows C:\Program Files\Chaos Group\V-Ray\V-Ray for SketchUp\extension\vrayappsdk\bin
macOS / Applications/ChaosGroup/V-Ray/V-Ray\ for\ SketchUp/extension/vrayappsdk/bin

Usage

Using the following command, converts the given .ply or .obj file and writes it to the given .vrmesh file. Note that you must specify the file extension; it is not added automatically.

> ply2vrmesh [options]

Arguments

inputFile – Specifies the .ply .obj .bin .geo (.hclassic) or .bgeo (.bhclassic) .abc .prt or .vrscene input file name. The string may include wildcards.

outputFile – Specifies .vrmesh file output name (extension must be specified). This string may not include wildcards. If this is not specified, then the output is a file with the same name but with the .vrmesh extension. If multiple input files are specified and is missing, then each input file will be written to a separate .vrmesh file. If multiple input files are specified and is also specified, all input files are sorted in lexical order and concatenated into one animated .vrmesh file.

Options

-verboseLevel – An integer value to determine the verbosity of the output. (0 — no output; 1 — errors only; 2 — errors and warnings; 3 — errors, warnings, and informational messages; 4 — all output). The default is 3.

-append – Appends the information as a new frame to the .vrmesh file.

-smoothNormals – Generates smooth vertex normals. Only valid for .obj and .geo files; always enabled for .bin files.

-smoothAngle – A floating point number that specifies the angle (in degrees) used to distinguish if the normals should be smoothed or not. If present, it automatically enables the -smoothNormals flag.

-flipNormals – Reverses the face/vertex normals. Only valid for .obj, .geo, .bin, and .abc files.

-flipVertexNormals – Reverses the vertex normals. Only valid for .obj, .geo, .bin and .abc files.

-flipFaceNormals – Reverses the face normals. Only valid for .obj, .geo, .bin, and .abc files.

-flipYZ – Swap y/z axes. Needed for some programs, i.e., Poser, ZBrush. Valid for .ply, .obj, .geo, and .bin files.

-flipYPosZ – Same as -flipYZ but does not reverse the sign of the z coordinate.

-flipXPosZ – Same as -flipYPosZ but swaps x/z axes.

-mapChannel – Stores the UVW coordinates to the specified mapping channel (default is 1). Only valid for .obj and .geo files. When exporting a mesh that will be used in Maya, currently, this must be set to 0, or the textures on the mesh will not render properly.

-disableColorSetPacking – Only valid for .geo and .bgeo files; disables the packing of float1 and float2 attributes in vertex color sets.

-materialIDs – Only valid for .geo and .bgeo files; assigns material IDs based on the primitive groups in the file.

-materialIDs_splitGroups – Only valid for .geo and .bgeo files; assigns material IDs based on the primitive groups. These groups are split into different voxels/meshes and appear in visibility lists.

-sortMaterialIDs – Only valid for .geo and .bgeo files; sorts the list of material IDs by the group name. Otherwise, they are in the same order as they appear in the .geo/.bgeo file.

-fps – A floating-point number that specifies the frames per second at which a .geo or .bin file is exported so that vertex velocities can be scaled accordingly. The default is 24.0.

-previewFaces – Specifies the maximum number of faces in the .vrmesh preview information. The default is 9973 faces.

-previewType – Specifies the method used to generate a preview.

clustering – Works very fast but is less accurate.
edge_collapse – Slower, but produces the best results.
combined – Fast, produces slightly better results than clustering.
face_sampling – Copies triangles from the original (very fast, but leaves a disconnected mesh).

-facesPerVoxel – Specifies the maximum number of faces per voxel in the resulting .vrmesh file. The default is 10000 faces.

-previewHairs – Specifies the maximum number of hairs in the .vrmesh preview information. The default is 500 hairs.

-segmentsPerVoxel – Specifies maximum segments per voxel in the resulting .vrmesh file. The default is 64000 hairs.

-hairWidthMultiplier – Specifies the multiplier to scale hair widths in the resulting .vrmesh file. The default is 1.0.

-previewParticles – Specifies the maximum number of particles in the .vrmesh preview information. The default is 20000 particles.

-particlesPerVoxel – Specifies maximum particles per voxel in the resulting .vrmesh file. The default is 64000 particles.

-particleWidthMultiplier – Specifies the multiplier to scale particles in the resulting .vrmesh file. The default is 1.0.

-mergeVoxels – Merge objects before voxelization to reduce overlapping voxels

-velocityAttrName – Specifies the name of the point attribute that should be used to generate the velocity channel. By default, the v attribute is used.

-pointSize – If specified, turns on point cloud generation and specifies the smallest size of the points. The default is 0.0 (point cloud generation is disabled).

-velocityOffset – Specifies that the starting position should be offset by a fraction of the velocity channel, e.g., -0.25. Only valid for .geo, .bgeo, and .bin files.

-mergeFiles – Merges all input files into one .vrmesh file.

Input files are specified using wildcard.
Output file (with .vrmesh extension) must be specified.

-mergeShaders – When merging files using -mergeFiles, this option merges all shaders with the same name into one shader. When merging .obj files, the first found .mtl file in the directory is parsed to get the ordering of the materials.

Alembic subdivision specific

-subdivideAllMeshes – Subdivides all alembic polygonal meshes, not only subdivision objects.

-subdivisionLevel – Alembic subdivision level.

-subdivideUVs – Specifies the subdivision of the mapping channels. Value 0 to skip map channel subdivision and 1 to apply it.

-preserveGeomBorders – Skips the subdivision for all geometry borders.

-preserveMapBordersMode – Preserves map borders mode.

Mode «none» to subdivide all map borders.
Mode «internal» to preserve internal borders.
Mode «all» to preserve all map borders.

*.vrscene specific

-vrsceneList – Shows a list of available Nodes in the .vrscene file.

-vrsceneNodeName – Node name inside the .vrscene file.

Must be specified!

-vrsceneApplyTm – Applies Node transform matrix to the mesh.

-vrsceneVelocity – Generates velocity channel (used for motion blur).

-vrsceneFrames start-end – Exports animation range.

-vrsceneWholeScene – Generates a proxy for all vrscene’s geometric objects.

Generic

-info – Shows information about the specified .vrmesh file.

-perObject – Prints additional information for each object in the file. Requires the -info flag.

-frame – Exports a particular frame from the specified file. Combined with -info option, it shows information about the specified frame from the .vrmesh file. Indices are 0-based. If this option is not specified, information is printed for each frame in the file.

-oneFramePerFile – Exports each frame in a separate file.

-padding – Frame padding number between 1 and 10. Default is 4.

These options can also be viewed from the command prompt by running the ply2vrmesh program without any parameters to see the description of these options.

Notes

  • The converter works with most of the popular .ply formats, both ASCII and binary, big-endian, or little-endian.
  • In addition to the geometric data (faces and vertices), the converter recognizes some of the most common additional channels such as diffuse surface color. Vertex colors are recognized if they are specified as «red», «green», and «blue» or «diffuse_red», «diffuse_green», and «diffuse_blue» vertex properties.

Introducing Object Capture

Turn photos from your iPhone or iPad into high‑quality 3D models that are optimized for AR using the new Object Capture API on macOS Monterey. Object Capture uses photogrammetry to turn a series of pictures taken on your iPhone or iPad into USDZ files that can be viewed in AR Quick Look, seamlessly integrated into your Xcode project, or used in professional 3D content workflows.

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Install macOS Monterey beta and use videos, documentation, sample code, and resources to create high‑quality and immersive AR content with Object Capture.

macOS Monterey and SDKs

Download macOS Monterey beta and Xcode 13 beta, which include support for the Object Capture API. View downloads

Create 3D models with Object Capture

Learn how to get started and bring your assets to life with the Photogrammetry API for macOS. Watch video

AR Quick Look, meet Object Capture

Discover simple ways to bring your Object Capture assets to AR Quick Look while optimizing for visual quality and file size. Watch video

Create 3D workflows with USD

Discover the flexibility, versatility, and power of Pixar’s Universal Scene Description (USD) for your 3D workflows. Watch video

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