I am currently exploring the notion of using iris in a project to read forecast grib2 files using python.
My aim is to load/convert a grib message into an iris cube based on a grib message key having a specific value.
I have experimented with iris-grib, which uses gribapi. Using iris-grib I have not been to find the key in the grib2 file, althrough the key is visible with 'grib_ls -w...' via the cli.
gribapi does the job, but I am not sure how to interface it with iris (which is what, I assume, iris-grib is for).
I was wondering if anyone knew of a way to get a message into an iris cube based on a grib message key having a specific value. Thank you
You can get at anything that the gribapi understands through the low-level grib interface in iris-grib, which is the iris_grib.GribMessage class.
Typically you would use for msg in GribMessage.messages_from_filename(xxx): and then access it like e.g. msg.sections[4]['productDefinitionTemplateNumber']; msg.sections[4]['parameterNumber'] and so on.
You can use this to identify required messages, and then convert to cubes with iris_grib.load_pairs_from_fields().
However, Iris-grib only knows how to translate specific encodings into cubes : it is quite strict about exactly what it recognises, and will fail on anything else. So if your data uses any unrecognised templates or data encodings it will definitely fail to load.
I'm just anticipating that you may have something unusual here, so that might be an issue?
You can possibly check your expected message contents against the translation code at iris_grib:_load_convert.py, starting at the convert() routine.
To get an Iris cube out of something not yet supported, you would either :
(a) extend the translation rules (i.e. a Github PR), or
(b) sometimes you can modify the message so that it looks like something
that can be recognised.
Failing that, you can
(c) simply build an Iris cube yourself from the data found in your GribMessage : That can be a little simpler than using 'gribapi' directly (possibly not, depending on detail).
If you have a problem like that, you should definitely raise it as an issue on the github project (iris-grib issues) + we will try to help.
P.S. as you have registered a Python3 interest, you may want to be aware that the newer "ecCodes" replacement for gribapi should shortly be available, making Python3 support for grib data possible at last.
However, the Python3 version is still in beta and we are presently experiencing some problems with it, now raised with ECMWF, so it is still almost-but-not-quite achievable.
Related
I want to use dataset at https://ingmec.ual.es/datasets/lidar3d-pf-benchmark/ in my project. The available map is .simplemap. What I understand is it stores both map and the robot poses as well. I want to get the point cloud representation of this map (which later I can convert into octomap) as well as vehicles ground truth pose in the map.
I have been able to get the CPose3DPDF from which I obtained CPose3d which I believe is the desired vehicle's ground truth pose. Please correct me if I am wrong. Now I have two problems. First the length of trajectory is just 97 which makes me suspicious about my code to obtain it. Second is about the CSensoryFrame which I obtain along with CPose3DPDF. When I get CObservation by doing CSensorFrame->getObservationByIndex and write to a file, it gives me idea that it stores velodyne readings. But I am unable to recover point cloud from it. Could anyone please guide me to a tool which can convert a .simplemap into a point cloud or an octomap representation and obtain vehicle's pose out of it as well. Many thanks in advance.
For the records: this one was answered here:
Your assumptions were all correct.
I realized the full UAL campus map was not included into the downloads. It's now available to download inside 2018-02-26-ual-campus-map.zip, at the bottom of this dataset page.
You can also regenerate the pointcloud, octomap from the .simplemap using the app application-observations2map.
Example .ini files can be found under MRPT/share/mrpt/config_files/*
You can also visually inspect .simplemap files with the robot-map-gui app.
I have an app that extracts information from incoming messages. The messages all contain the same information, but they have different forms depending on the source that sent them.
Example:
Message from source A :
A: You spent $50.00 at Macy's on 2/20/12
Message from source B :
Purchase, $50.00, Macy's, 2Feb2012, Balance $5000.00
Every message from a single source has the same form though. So at the moment, I'm doing it by writing a set of regular expressions to first identify which message I'm trying to decode (i.e. what source it came from so I know what the form of the message is), and then extracting the necessary information from the message (in the above example, I want to know the transaction amount, the store where the transaction happened, and the date). If I discover a new source for a message, or a source changes the format of their message (doesn't happen very often, but could happen), I need to manually write the regular expressions for that message. I'm sure however that I could automate this using some kind of machine learning technique. I just don't know much about machine learning, and I don't know where to even start looking for a technique that would apply to my problem. I would like someone to just point me in the right direction on where to start reading.
In order to detect and label amounts, dates, person names and similar information you can use a technique called Named Entity Recognition. The Stanford Named Entity Recognizer comes with pretrained, ready to use models.
You also use whatever labeled data you have generated so far to learn a custom model for your application. The standard techniques used for this purpose are Conditional Random Fields or Sequence Perceptron. There are many toolkits implementing these models, including:
Wapiti - A simple and fast discriminative sequence labelling toolkit.
Sequor - sequence labeler based on Collins's (2002) perceptron.
Don't know where to start on this one so hopefully you guys can clear up my question. I have project where email will be searched for specific words/patterns and stored in a structured manner. Something that is done with Trip it.
The article states that they developed a DataMapper
The DataMapper is responsible for taking inbound email messages
addressed to plans [at] tripit.com and transforming them from the
semi-structured format you see in your mail reader into a highly
structured XML document.
There is a comment that also states
If you're looking to build this yourself, reading a little bit about
Wrappers and Wrapper Induction might be helpful
I Googled and read about wrapper induction but it was just too broad of a definition and didn't help me understand how one would go about solving such problem.
Is there some open source project out there that does similar things?
There are a couple of different ways and things you can do to accomplish this.
The first part, which involves getting access to the email content I'll not answer here. Basically, I'll assume that you have access to the text of emails, and if you don't there are some libraries that allow you to connect java to an email box like camel (http://camel.apache.org/mail.html).
So now you've got the email so then what?
A handy thing that could help is that lingpipe (http://alias-i.com/lingpipe/) has an entity recognizer that you can populate with your own terms. Specifically, look at some of their extraction tutorials and their dictionary extractor (http://alias-i.com/lingpipe/demos/tutorial/ne/read-me.html) So inside of the lingpipe dictionary extractor (http://alias-i.com/lingpipe/docs/api/com/aliasi/dict/ExactDictionaryChunker.html) you'd simply import the terms you're interested in and use that to associate labels with an email.
You might also find the following question helpful: Dictionary-Based Named Entity Recognition with zero edit distance: LingPipe, Lucene or what?
Really a very broad question, but I can try to give you some general ideas, which might be enough to get started. Basically, it sounds like you're talking about an elaborate parsing problem - scanning through the text and looking to apply meaning to specific chunks. Depending on what exactly you're looking for, you might get some good mileage out of a few regular expressions to start - things like phone numbers, email addresses, and dates have fairly standard structures that should be matchable. Other data points might benefit from some indicator words - the phrase "departing from" might indicate that what follows is an address. The natural language processing community also has a large tool set available for text processing - check out things like parts of speech taggers and semantic analyzers if they're appropriate to what you're trying to do.
Armed with those techniques, you can follow a basic iterative development process: For each data point in your expected output structure, define some simple rules for how to capture it. Then, run the application over a batch of test data and see which samples didn't capture that datum. Look at the samples and revise your rules to catch those samples. Repeat until the extractor reaches an acceptable level of accuracy.
Depending on the specifics of your problem, there may be machine learning techniques that can automate much of that process for you.
Our customers use 500+ applications and we would like to integrate these applications with our. What is the best way to do that? These applications are time registration applications and common for most of them is that they can export to csv or similar, some of them are actually home-brewed excel sheets where time is registered.
The best idea so far is to create our own excel sheet, which can be used to integrate with all these applications. The integrations could be in the form of cells containing something like ='[c:\export.csv]rawdata'!$A$3 Where export.csv is the csv file exported from the time registration applications. Can you see a better way to integrate against all these applications? It should be mentioned that almost all our customers have Microsoft Office.
Edit: Answers to the excellent questions from Pontus Gagge:
How similar are the data in the different applications?
I assume that since they time registration applications, they will have some similarities, but I assume that some will register the how long time one has worked in total for a whole month, while others will spesify for each day. If Excel is chosen, I believe that many of the differences could be ironed out using basic formulas.
What quality is the data?
The quality of the data can vary so basic validation must be undertaken, a good way is also to make it transparent for the customers, how our application understands their input, so they are responsible.
How large amounts of data are you talking about?
There will be information about the time worked for up to 50 employees.
Is the integration one-way only?
Yes
With what frequency should information be transferred?
Once per month (when they need to pay salaries).
How often do the applications themselves change, and how often does your product change?
If their application is a home-brewed Excel sheet, then I assume it will change once a year (due for example a mistake someone). If it is a standard proper time registration application, then I do not believe they are updated more often than every fifth year or so, as it is a very stabile concept.
Should the integration be fully automatic or can your end users trigger a data transfer?
They can surely trigger data transfer. The users are often dedicated to the process so they can be trained at doing it, which means that they could make up to, say 30, mouse clicks in order to integrate each month.
Will the customers have somebody to monitor the integrations?
As we have many customers, many of them should be able to undertake the integration themselves. We will though be able to assist them over the telephone. We cannot, though undertake the integration ourselves because we would then be responsible for any errors due to user mistakes, etc.
Does the phrase 'integration spaghetti' mean anything to you...?
I am looking for ideas from the best chefs to cook a nice large portion of that.
You need to come up with a common data format, and a way to translate the individual data formats to the common format. There's really no way around this - any solution you come up with will have to do this in one way or the other. It's the essential complexity of what you're doing.
The bigger issue is actually variances within the source data, in terms of how things like dates are stored, missing columns, etc. Doing a generic conversion for CSV to move columns around is comparatively easy.
I would also look at CSV and then use an OLEDB connection against the CSV file for importing.
If you try to make something that can interface to any data structure in the universe (and 500 is plenty close enough), it is guaranteed to be a maintenance nightmare. Instead I would approach this from multiple angles:
Devise an interface into which a human can enter this data already in the proper format. With 500+ clients, I'd make this a small, raw but functional browser based site that users can use to enter this information manally. This is the fall-back. At the end of the day, a human can re-key the information into the site and solve the import issue. Ideally, everyone would use this instead of their own format. Data entry people are cheap.
Similar to above, but expanded, I would develop a standard application or standardize on an off-the-shelf application that can be used to replace their existing format. This might take more time than #1. The goal would be to only do one-time imports of these varying data schemas into the application and be done with them for good.
The nice thing about spreadsheets is that you can do anything anywhere. The bad thing about spreadsheets is that you can do anything anywhere. With CSV or a spreadsheet there is simply no way to enforce data integrity and thus consistency (which is the primary goal) on the data. If the source data is already in a database, then that is obviously simpler.
I would be inclined to use database format into which each of these files need to be converted rather than a spreadsheet (e.g. use something like Jet (MDB)). If you have non-Windows users then that will make it harder and you might have to use a spreadsheet. The problem is that it is too easy for the user to change their source structure, break their upload and come crying to you. If a given end user has a resident expert, they can find a way of importing the data into that database format . If you are that expert, then I would on a case-by-case basis, write something that would import into that database format. XML would be the other choice, but that will likely take more coding than an import/export into a database format.
Standardization of the apps (even having all the sources in a database format instead of a spreadsheet would help) and control over the data schema is the ultimate goal rather than permitting a gazillion formats. There really is no nice answer other than standardization. Otherwise, you are having to write a converter for every Tom-Dick-and-Harry format and again when someone changes the source format.
With a multitude of data sources mapping each one correctly to an intermediate format is not trivial. Regular expressions are good with a finite set of known data formats. Multipass can help when data is ambiguous without context (month,day fields and have several days of data), and also help defeat data entry errors. But it seems as this data is connected to salaries there needs a good reliable transfer.
An import configuring trick
Get the customer to make a set of training data in the application. It should have a "predefined unique date" and each subsequent data field have a number corresponding to the target data field in your application. On importing your application needs to recognise the predefined date, determine the unique translation required and effect the displaying/saving of this "mapping key", and stop the import. eg If you expect "Duration hours" in field two then get the user to enter 2 in the relevant field which might be "Attendance hours".
On subsequent runs, and with the mapping definition key, import becomes a fairly easy process of translation.
Note on terms
"predefined date" - must be historical, say founding date of your company?, might need to be in PC clock settable range.
"mapping key" - could be string of hex digits and nybble based so tractable to workout
The entered code can be extended to signify required conversions ie customer's application has durations in days and your application expects it in hours.
Interfacing with windows programs (in order if increasing fragility)
Ye Olde saving as CSV file
Print to operating system printer that is setup as a text file/pdf, then scavenge the data out of that
Extract data via the application interface control, typically ActiveX for several windows programs ie like Matlab's Spreadsheet Link
Read native file format xls format ie like Matlab's xlsread
Add an additional intermediate spreadsheet sheet that has extended cell references ie ='[filename]rawdata'!$A$3
Have a look at Teiid by JBoss: http://jboss.org/teiid
Also consider using SOA - e.g., if you're on Java, try JBoss SOA platform: http://www.jboss.com/resources/soa/?intcmp=1004
Use a simple XML format. A non-technical person can easily understand a simple XML format (and could even identify basic problems with XML documents that are not well-formed).
Maybe use a DTD (or even better an XML schema) to do very basic validation, and then supplement this with an XSL stylesheet to do more validation with better error reporting. (An XSL stylesheet simply converts from XML to something else and so can be generate readable error messages.)
The advantage of this approach is that web browsers such as Internet Explorer can apply the XSL stylesheets. A customer need only spend at most a day enhancing their applications or writing excel macros to generate the XML data in the format that you specify.
Recent versions of Excel have support for converting spreadsheet data to XML, and can even validate against schemas.
Once the data passes the XSL validation checks, you have validated XML data.
If you have heaps of data and heaps of money, you could look at existing data management and cleansing tools:
http://www-01.ibm.com/software/data/infosphere/datastage
http://www-01.ibm.com/software/data/infosphere/qualitystage
But even then, you'll likely need to follow kyoryu's suggestion assuming you have 500+ data formats. The problem isn't your side. You need them to standardize their output formats if you have no control over their apps. CSV is likely the easiest. You could even send them a excel template to help them along.
What I have to do
I'm trying to manipulate some rather large amounts of data stored in Excel files (one of the workbooks has as much as 150 spreadsheets). The result of these manipulations may yield approximately 800.000 rows in a database table.
The problem
Data stored in the spreadsheets has unpredictable format. The company that generated these spreadsheets had no fixed/documented format for exporting these files, and sometimes erroneous data appear. For example most of the years are represented like "2009" but there are cases where a year is represented as "20". Other example, data is not really normalized in these files, so I use separators to split the values of certain cells. Sometimes these separators change.
There are things like these that I couldn't predict and I only discovered them only after running an already evolved version of my program over a pretty large part of the available data.
The question
How can one test the correctness of a program in such a situation? Or rather, how to achieve a pretty stable version of the product without running it over the whole available data?
Shall I take a defensive approach and throw exceptions whenever some kind of unexpected issue arises? Then the main loop of the program may catch and log them and continue with the available data? This would yield some processed data, but that means that on a subsequent iteration of the program I have to have checks for what's already inside the database from previous iterations (which I don't really like).
What's your opinion? How would you tackle this problem?
If there is no specification for what the format of the data is, then anything is acceptable.
If not, then there is either an explicit or implicit specification of the data. I would try and nail this down right now. If you can't get an explicit enough definition of the data to write your program so that it can be expected to run without error, then I would say you are taking a very large risk in causing some serious damage depending on how this data is being used.
You should write your program so that it either throws an exception or logs an error whenever running across data that does not meet the specification. Then, run the program on PART of the available data until it runs without exception. This can be viewed as a training set for the development of your program. Then, use some of the saved data to use as a TEST set. This will give you an estimate of how many exceptions/errors your program will generate in production.
Overfitting is a common machine learning concept, but it is useful to other tasks such as this - program development. It is surprising to me how developers can write a bunch of unit tests, code their application to perform well on it, and then expect similar or bug-free performance in production.
If you're not willing to take all these steps (i.e. run your code on essentially all of the data -- since the test set is also making use of the data) then I would say the task is too large to do.
As an aside, rather than creating a definition of a format that is very strange and peculiar to account for all the "errors" in the current data, you might want to create a new, normalized (in the sense these things are simplified away) specification for the data, and then write a "faulty document patcher" that can be run on faulty documents to fix the data.
If the application generating the data is still in production, then you might need to go to the developers of this application to get a buy in on the new spec. Once you have that, you can then start logging bugs against their application, so hopefully the faulty document patcher can be retired.
More likely, I'm guessing that the software developers are long gone, no one understands the code anymore, if it is even running at all.
How can one test the correctness of a program in such a situation? Or rather, how to achieve a pretty stable version of the product without running it over the whole available data?
For every single data type I would set reasonable constraints on the values that it is allowed to be.
If a cell violates these constraints then throw an exception containing the piece of data it failed on and its data type. If a piece of data violated its constraints you can modify the source to include the additional constraints required for that piece of data, and a conversion method to make it uniform.
To give an example on the date you gave, initially a date would have the constraint that it could be only four digits. When the program came across the "20" it would throw an exception.
Then you could go and allow two digit dates, and a method to convert the two-digit dates into a four digit one to allow further processing.
One question is, will you run your program more than once? From your question it sounds possible you only want to run it once, and then you will then work with the data in the database.
In which case you can be very defensive - throw exceptions whenever unexpected data appears. Run the program repeatedly on ever-larger sets of the data. Initially, solve any exceptions by altering the code, as it's a good rule of thumb that the exceptions you find first are going to be common. You might want to empty the output database between runs.
Later on, you will be finding rare exceptions that might only occur a couple of times in the input. Just solve these by hand and insert the corresponding rows in the database yourself. Or write another small program that reads your exception information and inserts the new rows, rather than running your whole big program again.
Typically for this sort of thing I do these as #MarkJ suggested, and I encode the whole thing in unit tests.
So I compose a small datafile that at first contains only a few rows of normal data. That's unit test number 1.
Then I take a quick visual scan of some of the data to spot any obvious exceptions. Unit tests 2 through n.
Finally, I write parser code until it passes all unit tests, and throws and logs exceptions for all un-managed data.
I then use these oddball bits of data to make new unit tests, and improve the parser until it can pass those too.
Although sometimes accommodating some really strange bit of data adds more parser complexity than it's worth, and I'll just log the exception, dump it, and move on. This is a matter of professional judgment.
How about processing every piece of data (so you don't have to check for dupes). Those that pass go into the database. The exceptions go into an exception file. The user can open the exception file and make corrections/modifications to the data. Then they can run your program on the exception file.
This will isolate unhandled data for the user to correct and prevent you from processing the same data twice (or more).