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R语言处理.zim文件（ZooImage元数据/度量）zimExtractAll()函数-中英文对照帮助文档
By MicroRbt Martinez PhD
R语言函数名：zimExtractAll()
R语言函数功能：处理.zim文件（ZooImage元数据/度量）
来自资源库：CRAN
zimExtractAll()函数所属R语言包：所在R包具体名称、包功能的中英文双语描述见正文后面'--所在R语言包信息--'部分。
描述-----Description-----
Various fonctions to manipulate ZooImage Metadata in .zim format (either '*.zim', or '*_datX.zim' files).
多种功能以.zim格式（“ * .zim”或“ * _datX.zim”文件）操作ZooImage元数据。
使用方法-----Usage-----
zimCreate(zimfile, template = NULL, edit = TRUE, editor =
getOption("fileEditor"), wait = FALSE)
zimEdit(zimfile, editor = getOption("fileEditor"), wait = FALSE, ...)
zimMake(dir = ".", pattern = extensionPattern("tif"), images =
list.files(dir, pattern))
zimExtractAll(zipdir = ".", zipfiles = zipList(zipdir), path = NULL,
replace = FALSE)
zimUpdateAll(zipdir = ".", zipfiles = zipList(zipdir), zimdir = NULL,
check.zim = TRUE)
isZim(zimfile)
zimVerify(zimfile, is.dat1 = hasExtension(zimfile, "_dat1.zim"),
check.table = FALSE)
zimDatMakeFlowCAM(zimfile)
zimDatMakeFlowCAMAll(path = ".", zimfiles = NULL)
参数-----Arguments-----
参数zimfile介绍: a .zim file.
.zim文件。
参数zimfiles介绍: a list of .zim files to use.
要使用的.zim文件列表。
参数template介绍: a .zim template to start with, if the .zim file does not exist yet.
如果.zim文件尚不存在，则以.zim模板开头。
参数edit介绍: do we edit the .zim file that we just created?
我们如何编辑刚刚创建的.zim文件？
参数editor介绍: a program to use for editing the .zim file.
用于编辑.zim文件的程序。
参数wait介绍: do we wait that the file is edited? In this case, R is frozen until the editor is closed.
我们等待文件被编辑吗？在这种情况下，R将冻结直到关闭编辑器。
参数dir介绍: a directory where .zim files will be created.
将在其中创建.zim文件的目录。
参数pattern介绍: the pattern matching for automatically listed images that require a .zim file.
自动列出的需要.zim文件的图像的模式匹配。
参数images介绍: the list of images requiring a .zim file (either all image matching 'pattern' in 'dir', or provide your own listing here).
需要.zim文件的图像列表（“ dir”中所有与“ pattern”匹配的图像，或在此处提供您自己的列表）。
参数zipdir介绍: a directory where to find .zip files.
查找.zip文件的目录。
参数zipfiles介绍: a list of .zip files (by default, all .zip files in 'zipdir').
.zip文件列表（默认情况下，“ zipdir”中的所有.zip文件）。
参数path介绍: the path where to extract zims. If NULL, it is computed from zipdir: it is either the same path, or the parent directory if last directory is named '_raw'.
提取zims的路径。如果是NULL，则从zipdir计算得出：它是相同路径，或者如果最后一个目录名为“ _raw”，则为父目录。
参数replace介绍: do we replace existing .zim files?
我们如何替换现有的.zim文件？
参数zimdir介绍: the directory where the .zim files are located.
.zim文件所在的目录。
参数check.zim介绍: do we verify .zim files before refreshing metadata in .zip files?
在刷新.zip文件中的元数据之前，我们如何验证.zim文件？
参数is.dat1介绍: is it a '\_dat1.zim' file, that is a file collecting metadata AND objects measurements?
是'\ _dat1.zim'文件，即收集元数据和对象测量值的文件吗？
参数check.table介绍: try to read the table of measurements in the '[Data]' section. Ignored if is.dat1 = FALSE.
尝试读取“ [数据]”部分中的测量表。如果is.dat1 = FALSE被忽略。
参数...介绍: further arguments passed to the fileEdit().
进一步的论点传递给了fileEdit()。
详情-----Details-----
ZooImage Metadata/Measurements ('.zim' and '_dat1.zim' files, respectively) are text files containing metadata (that is, additional information required to process the images, like sample identification, information about collection and process of the sample, digitizing hardware and software, etc.). These metadata are represented as a pair 'key' = 'value' in ANSI encoding and are organized into sections written in square brackets on a separate line. For instance, '[Subsample]' defines a 'Subsample' section. The first line of .zim files must always be 'ZI1' in the case of ZooImage version 1, 'ZI2' for version 2, and 'ZI3' for current version. This identifiant allows for making incompatible changes in future versions without taking the risk to accidentally try processing these newer versions with an old, incompatible version of ZooImage in the future. Here are the first few lines of an example .zim file: for instance).
ZooImage元数据/度量（分别为'.zim'和'_dat1.zim'文件）是包含元数据的文本文件（即，处理图像所需的其他信息，例如样品识别，有关样品收集和处理的信息，数字化硬件和软件等）。这些元数据在ANSI编码中表示为一对“键” =“值”，并组织在用方括号括起来的小节中。例如，“ [Subsample]”定义了“ Subsample”部分。对于ZooImage版本1，.zim文件的第一行必须始终为“ ZI1”，对于版本2，“ ZI2”，对于当前版本为“ ZI3”。此标识允许在将来的版本中进行不兼容的更改，而不必冒将来冒用旧的不兼容版本的ZooImage意外处理这些较新版本的风险。这是示例.zim文件的前几行：
After 'ZI3' in the first line, there is a definition of an 'Image' section, with two keys: 'Hardware' with value 'EPSON 4870' and 'Software' with value 'VueScan 8.0.10', followed by a comment (everything after the '#' sign). Take care: since '#' defines a comment, do not use it, neither in keys, nor in values!
在第一行的“ ZI3”之后，有一个“图像”部分的定义，带有两个键：值为“ EPSON 4870”的“硬件”和值为“ VueScan 8.0.10”的“软件”，后跟注释（“＃”符号后的所有内容）。注意：由于“＃”定义了注释，因此无论是在键中还是在值中都不要使用它！
Take care to define unique keys accross all sections! The section are just there to organize your metadata into logical subunits... but they are not considered in the process. If you define a key named 'mykey' both in '[Section1]' and in '[Section2]', only the first occurence of 'mykey' will be used by ZooImage!
注意在所有部分定义唯一的键！该部分仅用于将元数据组织为逻辑子单元...但是在此过程中不考虑它们。如果在“ [Section1]”和“ [Section2]”中都定义了一个名为“ mykey”的键，则ZooImage仅会使用“ mykey”的首次出现！
The ZooImage Measurements ('_dat1.zim' files) are structured the same way, but there is a special '[Data]' section at the end that contains a tab-delimited table with all measurements done on identified objects, during the image analysis (process of the images). This table starts with a header naming the colums, with two first columns being necessary '!Item' and 'Label'. 'Label' is the name of the image where the object is found and 'Item' is a unique identifier (usually a number) given to that object in the image (i.e., Label+Item is the unique identifier of each object in the whole series). The other columns define the measurements done on the objects (area, perimeter, length, distribution of gray levels, etc.). The amount and name of measurements are not fixed. It is the particular ImageJ plugin that you use to process your image that defines them (it means that adding new measurements is very easy to do and they are automatically considered by ZooImage).
ZooImage Measurements（“ _ dat1.zim”文件）的结构相同，但是在图像分析期间，末尾有一个特殊的“ [Data]”部分，其中包含制表符分隔的表，其中所有对确定的对象进行的测量（图像处理）。该表以命名列的标题开头，前两列是必需的“！Item”和“ Label”。 “标签”是在其中找到对象的图像的名称，“项目”是在图像�
-----未完，待续-----，↓↓↓展开剩余72%↓↓↓
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发表于 2020-10-6 07:30:52
