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Fortran: Data file Format Guide for ANUSPLIN
lixujeremy 2015-9-18 21:49
Summary 开贴记录 ANUSPLIN 输入文件的 Fortran 数据格式定义规范。输入数据格式非常重要,它直接决定着 ANUSPLIN 模块是否运行及录入数据是否正确,有时出现错误 RDATA - INPUT DATA FILE ERROR ,或由于存储及读入格式匹配不当而引发 SPLINA - TOO FEW DATA POINTS 错误。这里有必要格外强调一下 Fortran 数据输出及输入之格式定义。 Example 这里以 Temp 示例中第一条命令要求的数据文件 tmaxa.dat 为例说明格式匹配问题。 命令文件 tmaxa.cmd 中指定 tmaxa.dat 以 (a20,2f10.3,f8.1/12f7.1) 格式读入,那么 tmaxa.dat 就必须以上述格式写入 .dat 文件,观察 tmaxa.dat 文件如 Fig. 1 所示: Fig. 1 先解析 a20,2f10.3,f8.1/12f7.1 的意义(参考 ANUSPLIN Format Specification ), 20 位字符、 2 个 10 位数字(小数点后 3 位)、 8 位数字(小数点后 1 位)、换行( / ) 12 个 7 位数字(小数点后 1 位)。返回来看 Fig. 1 ,任何一条站点的第一行必定是 20+2*10+8=48 占位,任何一条站点第二行也必定是 12*7=84 占位,例如第 11 行,站点 Label 长度只有 9 位,其他 11 位以空格代之(空格是有意义的),随后紧跟着 145.550 (总共 7 位),其他 3 位以空格代之, Fortran 在这一行先以前 20 位认为是字符,往后 10 位是数值,再后还是 10 位数值,再再后是 8 位数值,空格、小数点、负号都有占位意义。 所以我们明白第二行在 Fortran 看来是 7 位一个数字,按照这样的数据文件与 .cmd 文件格式声明才能让 Fortran 语言编写的 ANUSPLIN 正确读入数据。 Test 按照前文描述的数据文件与命令文件格式声明的匹配事项,编辑 tempY1991.dat 与 tempY1991.cmd 文件测试,测试结果运行良好, ANUSPLIN 正确读入数据并完成相关配置要求。 SOLUTION.rar
个人分类: Fortran|4442 次阅读|0 个评论
[转载]IDL+Matlab:Read ENVI Standard File
lixujeremy 2014-10-18 09:37
我 Google 代码时,找到美国 Carl Salvaggio 教授在网上分享的 IDL 和 Matlab 代码,实现 IDL (不借助 ENVI 函数)和 Matlab 读取 ENVI Standard 文件。代码经测试,全部可以读取 N 波段的 ENVI Standard 文件,返回数据集矩阵。 附上练习数据及代码( Practice.rar )。 Carl Salvaggio 教授的兴趣在于遥感数字图像的处理,更多他个人代码的介绍和下载地址: here 。
个人分类: ENVI/IDL|4681 次阅读|0 个评论
cdsStartStat, cdsEndStat, exonFrames of GenePredExt format
bigdataage 2014-10-8 17:50
cdsStartStat, cdsEndStat, exonFrames of GenePredExt format gpe格式的最后一列是exonFrames,一列逗号隔开的数,可以取{0,1,2}或是-1。 -1,代表对应的exon全部位于UTR区,不参与翻译。 {0,1,2},代表对应的exon在参与翻译时,需要向前一个exon的末尾取n={0,1,2}个碱基,从而组成正确的读码框。这里说的前一个exon,和转录本所在链方向一致,即5'端的exon。 因此,第一个coding exon的exonFrame必然是0,不因start codon在这个exon内部的位置而变。 使用exonFrames的时候一定要参考到转录本方向,否则信息全都会错掉。 倒数第二列 cdsEndStat 和倒数第三列 cdsStartStat: string cdsStartStat; enum('none','unk','incmpl','cmpl') string cdsEndStat; enum('none','unk','incmpl','cmpl') These fields provide additional information about the status of the start and end of a gene's coding region. The possible statuses are: - none - no CDS specified from the sequence's data source. - unk - unknown - not known if CDS start/end is complete. - incmpl - the CDS start/end is incomplete - cmpl - the CDS start/end is complete. 来源: http://yanshouyu.blog.163.com/blog/static/2142831822014218104913372/ http://redmine.soe.ucsc.edu/forum/index.php?t=msggoto=3414S=04f4b46d643063e6206cf7564edf8460
8015 次阅读|0 个评论
Thomson Reuters数据引用的格式
tuic 2012-11-7 10:17
Thomson Reuters 建议将该资源引用为: Roper Center (1947): Roper Center for Public Opinion Research. Roper Center for Public Opinion Research. http://www.ropercenter.uconn.edu/ Crous, Pedro; Braun, Uwe; Hunter, Gavin C; Wingfield, Michael; Verkley, G.J.M.; Shin, Hyeon-Dong; Nakashima, Chiharu; Groenewald, Johannes (2013): Phylogenetic lineages in Pseudocercospora. TreeBASE. http://treebase.org/treebase-web/search/study/summary.html?id=12805 从该引用格式上看,基本上还是遵从了数据引用的格式,内容涵盖了其作者(creator),出版年(publication year),数据标题(title),出版机构(publisher),访问地址(URL)的信息,我想今后这种引用格式将成为主流,应该得到广大科研工作者的共识。
5151 次阅读|0 个评论
【Fortran】format语句中如何指定重复数目的格式描述符
热度 1 ddbb12 2011-10-12 09:37
好久没有写过与fortran程序相关的东西了。Fortran语言作为至今仍在研究界有很大的市场,因其语法简单,规则较少,使用灵活,的确是吾辈求解方程、数值模拟的一大神器。具体的关于Fortran语言的介绍和基本规则,可参考很多的参考书和搜索引擎。笔者本人学习的是 《 Fortran 95 程序设计》彭国伦 ,可参考本博书评。 昨天想到了这样一个问题: 例如,有一个可变数组(allocatable array)是N维的,dimesion :: a(N), 如果N=10,那么可以用 write(*,100)(a(i)i=1,10) 100 format(10(I3)) 之类的代码来进行输出操作。 但是,如果一旦N发生变化,那么只有修改format语句才能正确输出。而且,为了保持所有平台的兼容性,应该要求每次N发生变化的时候,都应该修改代码。这有失一般性。 那么 有没有可能在fortran的format语句中用变量来表示描述符的个数, 或者说, 有没有可能将format写成: format(N(I3))之类的格式呢? 实际上这个问题可以有多种解决途径: 1、 据说在CVF下可以使用一个尖括号来写成如nI3,从而来表示可变的重复次数。CVF的手册上也是如此说的,但是由于没有环境,因此没有做过测试。 2、可先设计一个不限长度的字符串,然后通过显示循环,将要输出的a(i)的每个元素都以内部文件的形式写入该字符串中。最后只需要输出该字符串即可。 3、实际上最后解决问题的方法是这样的,只需要将format中这个要重复描述符前面的这个数字设计成一个比待输出的元素个数的大的整数即可。该方法已经在gfortran下调试通过,没有任何错误。 当然,这种方法也有缺陷,如果这些重复输出元素不是输出列表中的最后一项就会出现格式错乱。、 话说,格式这种事情本来就很容易的错乱的。人们总是希望输出的东西好看,整齐,有规律,所以才有了格式这个玩意。Anyway,也算是个小问题。
个人分类: 计算机|12969 次阅读|1 个评论
What’s UDF?
putin24 2010-11-4 19:02
When I have burnt DVD optical disks using Nero Software which is a famous optical disk-burning software, unfortunately I came across a big single xxx.avi Media file which can't be burnt by ISO format. So as to I tried another file format system called UDF. What'sthe UDF,introduction as follows: Universal Disk Format (UDF) is an implementation of the specification known as ISO/IEC 13346 and ECMA-167 and is an open vendor-neutral file system for computer data storage for a broad range of media. In practice, it has been most widely used for DVDs and newer optical disc formats, supplanting ISO 9660. Due to its design, it is very well suited for incremental updates on both recordable or (re)writable optical media . UDF is developed and maintained by the Optical Storage Technology Association (OSTA 组织 ). Normally, authoring software will master a UDF file system in a batch process and write it to optical media in a single pass. But when packet writing to rewriteable media, such as CD-RW, UDF allows files to be created, deleted and changed on-disc just as a general-purpose file system would on removable media like floppy disks and flash drives . This is also possible on write-once media, such as CD-R, but in that case the space occupied by the deleted files cannot be reclaimed (and instead becomes inaccessible). Multi-session mastering is also possible in UDF, though some implementations may be unable to read disks with multiple sessions. Universal Disk Format builds are as follows: 1)Plain (Random Read/Write Access). This is the original format supported in all UDF revisions 2)Virtual Allocation Table a.k.a. VAT (Incremental Writing). Used specifically for writing to CD-R and (write-once) media 3)Spared (Limited Random Write Access). Used specifically for writing to CD-RW and DVD-RW (rewritable) media UDF version 1.02 1.50 2.0x 2.50 2.60 Windows XP/Server 2003 yes yes yes no no
个人分类: 技术研究|3391 次阅读|0 个评论
转:The IMRAD Research Paper Format
wangshilei 2009-12-19 21:18
原文地址: http://www.uta.fi/FAST/FIN/RESEARCH/imrad.html When discussing academic writing, one often hears about the IMRAD format. What is this format? IMRAD ( I , M ethods, R esearch D iscussion ) is a mnemonic for a common format used for academic research papers. While used primarily in the hard sciences, like physics and biology, it is also widely used in the social and behavioral sciences. The IMRAD format is also known as the APA format , as the American Psychological Association employs the IMRAD headings in its APA stylesheet. IMRAD is simply a more 'defined' version of the IBC format used for all academic writing. ntroduction Research in the Humanities normally uses a style which is similar to IMRAD, in the sense that academic research in all fields follows common principles of explication. However, the focus in Humanities research is more on readability and the clarification of nuances within the topic , with a less-distinct separation of topic explication and 'exact' data collection procedures than would be appropriate for research in the hard sciences. Further, in the Humanities generally, as well as in the English Section, MLA (Modern Language Association) style is preferred over APA style. There may also be 'house styles' employed by a particular institution (or university department/program) for publication consistency. The format used for the FIN-1 paper is a 'house style' Humanities-oriented IMRAD modification enhanced for readabililty and clarity of presentation in the HTML format in which the papers will be published. A Brief IMRAD Research Example Following is an example of using the IMRAD format for a report based on field research concerning the 21 September 2007 car-free day events at Tampere University. The research question is: How did students at Tampere University feel about the car-free day? Your research based on observation, interviews and/or surveys will provide the data to answer the question. Your answer will be a hypothesis (proposed thesis) that you will attempt to prove. Your data will be the evidence for your 'proof'. The IMRAD format would include the following basic sections, as modified to fit the FIN-1 HTML publication standard. (NB: Some other sections, such as the paper's Conclusion, are not included in the IMRAD mnemonic.) Introduction (including a title) The title is centered at the top of the first page. Below the title, but without a heading of its own , is the introductory section. This comprises one or several paragraphs which outline the research question and its significance within the topic being discussed, making it clear what the relevance of the question and topic are for readers of the paper. What is the history of the car-free day? Who sponsors it, and why? Who/what are these organizations? How long have there been 'car-free days'? How widespread is the concept in Tampere or Finland (perhaps as opposed to other cities or countries)? How 'successful' have past events been (as defined by what criteria)? In what sense might the event or its concept be controversial (in whose eyes, and why)? (etc.) Method Describe how you gathered the information. What events did you observe involving university students, teachers and staff during the car-free day? Who did you interview? Why did you interview these particular people? What sort of information did you expect to get from them? If you interviewed people who didn't observe the car-free day, where did you find them? What did you expect they'd tell you? Were attitudes of university students, teachers and staff different from those of other residents of Tampere? In what ways? How do you know? If your paper includes interviews or surveys, here is where you would describe their design and procedure. Results What did you find out from the method you had employed? Here's where you would include your description of the recent car-free day, and the various opinions received by different means from different respondents. This is the main section of your paper. Discussion What do the findings presented under Results above mean? Specifically, how do your findings prove your thesis? What patterns do you see in the data? How do they correlate with what had been 'known' about the event, and/or what you had expected to find? Did you find what you had expected to, or were you surprised? (Often the parts that surprised you are the most significant, and the most interesting.) Is further research desirable? If so, what, and how? Researchers often use this section to promote interest (and funding) for their next research project. Limitations on the Research Design and Material Often a separate subdivision of the research discussion is a description of the limitations inherent in your research method, the material available for the research, or other such factors. Viewed after the fact, what would you have done differently (if you had been able to) to obtain more objective and 'reliable' results? All research projects will have such limitations: this does not diminish the findings of what was discovered, confirmed or disproved with the plan and material which was used; it simply recognizes that, had it been possible to conduct the project differently (with more complete material, a longer time frame, etc.) the results could or would have been different. Conclusion, Notes, Works Cited and Appendices While the IMRAD format presumes the paper's conclusion to be a subsection of the Discussion, there should be a distinct closing to the paper of several paragraphs that briefly summarize what the paper has proposed, discussed and concluded. Following this would be (in MLA format) possible Notes, the paper's Works Cited, and possible Appendices. FIN-1 Examples of the Optional Research Component As examples of how past FIN-1 students have incorporated research components into their papers, using the conceptional development illustrated above, see (among others) Tove Jansson, The Moomin Business and Finnish Children (Rih 2005), Media Education in Finnish Upper Secondary Schools (Silvennoinen, 2005), Elk Hunting and Elk Hunters in Finland (Turunen, 2006), First-Born Laestadianism in Finland (Hartikka, 2007), and The Prospective Difficulty of Integrating Islamic Immigrant Labor Into Finnish Society (Karra, 2007). Other References on the IMRAD Format Further detail on IMRAD style may be obtained from the following links. Note that most concern the hard and behavioral sciences, and most include Abstracts and other related material to the standard IMRAD sections. An overview of the IMRAD format in a handout from the Writing Center of the University of Wisconsin at Madison at http://www.wisc.edu/writing/Handbook/ScienceReport.html . There are links to more detailed explanations of each of the headings, too. A PDF overview from the Harvard University School of Public Health on Credibility, Argument, and Structure in Public Health Writing which presents the IBC variation on the IMRAD format, and emphasizes the need for reader-orientation of academic research writing. The biology department at George Mason University has a good overview of writing scientific papers, with links to separate pages on the introduction, method, results and discussion sections. The overview and links are at http://classweb.gmu.edu/biologyresources/writingguide/ScientificPaper.htm
个人分类: 学术素养|4558 次阅读|0 个评论

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