I have some trouble understanding the value of Time (0040,A122) tag. I am trying to update an anonymization software, but I can't seem to find any example of the actual tag.
The DICOM standard (PS 3.3) mentions that:
This is the Value component of a Name/Value pair when the Concept implied by Concept Name Code Sequence (0040,A043) is a time.
Note
The purpose or role of the date value could be specified in Concept Name Code Sequence (0040,A043).
Required if the value that Concept Name Code Sequence (0040,A043) requires (implies) is a time. Shall not be present otherwise.
So basically Concept Name Code Sequence (0040,A043) specifies what type of time it is? I would like to know what are some examples of Concept Name Code Sequence?
I would suggest to have a look at the SR sample given from the DICOM standard section PS 3.20:
A.7.2 Target DICOM SR "Measurement Report" (TID 1500)
In particular:
>>>>1.5.1.1.4: HAS ACQ CONTEXT: TIME: (111061,DCM,"Study Time") = "070844"
You may also want to check PS 3.16 for the definition of TID 1500:
TID 1500 Measurement Report
Just as a reminder, Enhanced SR are defined in PS 3.3:
A.35.2 Enhanced SR IOD
Related
I am attempting to solve the Google ASP Competition 2019 : Insurance Referee Assignment problem. The problem is provided in this link.
There is a hard constraint that if a referee has preference type of 0 then the case will not be assigned to that referee. I have simplified the problem to include a few variables.
case(cid) refers to a case with cid as the case id.
ref(rid) refers to the referee with referee id.
pref(rid, type) takes the preference of referee 'rid' and type which takes value from 0 to 3. The higher the number, the more likely it will take the case.
In ref(10, 3) and ref(9, 2), the higher preference will be given to ref(10).
I have tried the following clingo code:
ref(rid).
case(cid).
pref(rid, type).
assign(cid, rid) :- ref(rid), pref(rid, type), type != 0.
case(4).
ref(3).
ref(5).
pref(3, 0).
pref(5, 1).
#show assign/2.
However, when I run the command, it shows satisfiable but outputs only this
assign(cid, rid)
What am I doing wrong?
In clingo variables start with a capital letter and are "valid" just withhin the rule. So my guess is you want the following code:
assign(Rcid, Rrid) :- case(Rcid), ref(Rrid), pref(Rrid, Rtype), Rtype != 0.
case(4).
ref(3). ref(5).
pref(3, 0). pref(5, 1).
#show assign/2.
output:
Solving...
Answer: 1
assign(4,5)
SATISFIABLE
Please note that only renaming the constants to variable names will result in an error message, you have to add case(Rcid) to the rule body as well. Variable names were freely choosen, you can use any variable name as long as it starts with a capital letter.
I have a one hdf5 format file Data File containing the molecular dynamics simulation data. For quick inspection, the h5ls tool is handy. For example:
h5ls -d xaa.h5/particles/lipids/positions/time | less
now my question is based on the comment I received on the data format! What attributes are missing according the hdf5 specifications and metadata in group?
Are you trying to get the value of the Time attribute from a dataset? If so, you need to use h5dump, not h5ls. And, the attributes are attached to each dataset, so you have to include the dataset name on the path. Finally, attribute names are case sensitive; Time != time. Here is the required command for dataset_0000 (repeat for 0001 thru 0074):
h5dump -d /particles/lipids/positions/dataset_0000/Time xaa.h5
You can also get attributes with Python code. Simple example below:
import h5py
with h5py.File('xaa.h5','r') as h5f:
for ds, h5obj in h5f['/particles/lipids/positions'].items():
print(f'For dataset={ds}; Time={h5obj.attrs["Time"]}')
DM scripting beginner here, almost no programming skills.
I would like to know the commands to access all the metadata of DM images/spectra.
I realized that all my STEM images at 80 kV taken between 2 dates (let's say 02.11.2017-05.04.2019) have the scale calibration wrong by the same factor (scale of all such images needs to be multiplied by 1.21).
I would like to write a script which multiplies the scale value by a factor only for images in scanning mode at 80 kV taken during a period for all images in a folder with subfolders or for all images opened in DM and save the new scale value.
I checked this website http://digitalmicrograph-scripting.tavernmaker.de/other%20resources/Old-DMHelp/AllFunctions.html but only found how to call the scale value (ImageGetDimensionCalibration). I have a general idea how to write the script based on other scripts if I find out how to call the metadata.
If anyone can write the whole script for me I would greatly appreciate your effort.
All general meta-data is organized in the image tag-structure
You can see this, if you open the Image Display Info of an image. (Via the menu, or by pressing CTRL + D) and then browse to the "Tags" section:
All info on the right are image tags and they are organized in a hierarchical tree.
How this tree looks like, and what information is written where, is totally open and will depend on what GMS version you are using, how the hardware is configured etc. Also custom scripts might alter this information.
So for a scripting start, open the data you want to modify and have a look in this tree.
Hint: The following min-script can be useful. It opens a tag-browsing window for the front-most image but as a modeless dialog (i.e. you can keep it open and interact with other parts):
GetFrontImage().ImageGetTagGroup().TagGroupOpenBrowserWindow(0)
The information you need to check against is most probably found in the Microscope Info sub-tree. Here, usually all information gathered from the microscope during acquisition is stored. What is there, will depend on your system and how it is set up.
The information of the STEM image acquisition - as far as the scanning engine and detector is concerned - is most probably in the DigiScan sub-tree.
The Data Bar sub-tree usually contains date and time of creation etc.
Calibration values are not stored in the image tag-structure
What you will not find in this tag-structure is the image calibration, i.e. the values actually used by DM to display calibrated values. These values are "one level up" so to speak here:
This is important to know in the following for your script, because you will need different commands for both the "meta-data" from the tags, and the "calibration" you want to change.
Accessing meta-data by script
The script-commands you need to read from the tags are all described in the F1 help documentation here:
Essentially, you need a command to get the "root" TagGroup of an image, which is ImageGetTagGroup() and then you traverse within this tree.
This might seem confusing - because there are a lot of slightly different commands for the different types of stored tags - but the essential bits are easy:
All "Paths" through the tree are just the individual names (typed exactly)
For each "branch" you have to use a single colon :
The commands to set/get a tag-value all require as input the "root" tagGroup object and the "path" as a string. The get commands require a variable of matching type to store the value in, the set commands need the value which should be written.
= The get commands themeselves return true or false depending on whether or not a tag-path could be found and the value could be read.
So the following script would read the "Imaging Mode" from the tags of the image shown as example above:
string mode
GetFrontImage().ImageGetTagGroup().TagGroupGetTagAsString( "Microscope Info:Imaging Mode", mode )
OKDialog( "Mode: " + mode )
and in a little more verbose form:
string mode // variable to hold the value
image img // variable for the image
string path // variable/constant to specify the where
TagGroup tg // variable to hold the "tagGroup" object
img := GetFrontImage() // Use the selected image
tg = img.ImageGetTagGroup() // From the image get the tags (root)
path = "Microscope Info:Imaging Mode" // specify the path
if ( tg.TagGroupGetTagAsString( path, mode ) )
OKDialog( "Mode: " + mode )
else
Throw( "Tag not found" )
If the tag is not a string but a value, you will need the according commands, i.e.
TagGroupGetTagAsNumber().
I am trying to set up a transformer on a Database Reader to file writer channel. I am reading in a sql field called MRN which I would like to send to a variable called mrn. I added a step to a channel with a variable called tmp['MSH'] mapping to a variable called msg['MSH'] But mirth is giving me the error message:
The variable name contains invalid characters. Please enter a new variable name
What are the rules for a valid variable name in mirth?
tmp and msg are two built-in variables containing E4X mappings of the outbound template and inbound message, respectively. You would map, via a MessageBuilder step, from inbound to outbound with tmp['MSH'][...] = msg['MSH']... where ... refers to the appropriate sections. Essentially these are pre-populated javascript property arrays.
If you really want to create a variable for use in multiple places, the rules are alphanumeric plus '_', I believe.
In a MessageBuilder step, you could refer to a previously created variable with ${varname}.
I would recommend investing a little time in getting familiar with the basics. Documentation is wanting, to be sure, but this blog post series are a good place to start.
I ran into a strange statement when working on a COBOL program from $WORK.
We have a paragraph that is opening a cursor (from DB2), and the looping over it until it hits an EOT (in pseudo code):
... working storage ...
01 I PIC S9(9) COMP VALUE ZEROS.
01 WS-SUB PIC S9(4) COMP VALUE 0.
... code area ...
PARA-ONE.
PERFORM OPEN-CURSOR
PERFORM FETCH-CURSOR
PERFORM VARYING I FROM 1 BY 1 UNTIL SQLCODE = DB2EOT
do stuff here...
END-PERFORM
COMPUTE WS-SUB = I + 0
PERFORM CLOSE-CURSOR
... do another loop using WS-SUB ...
I'm wondering why that COMPUTE WS-SUB = I + 0 line is there. My understanding is that I will always at least be 1, because of the perform block above it (i.e., even if there is an EOT to start with, I will be set to one on that initial iteration).
Is that COMPUTE line even needed? Is it doing some implicit casting that I'm not aware of? Why would it be there? Why wouldn't you just MOVE I TO WS-SUB?
Call it stupid, but with some compilers (with the correct options in effect), given
01 SIGNED-NUMBER PIC S99 COMP-5 VALUE -1.
01 UNSIGNED-NUMBER PIC 99 COMP-5.
...
MOVE SIGNED-NUMBER TO UNSIGNED-NUMBER
DISPLAY UNSIGNED-NUMBER
results in: 255. But...
COMPUTE UNSIGNED-NUMBER = SIGNED-NUMBER + ZERO
results in: 1 (unsigned)
So to answer your question, this could be classified as a technique used cast signed numbers into unsigned numbers. However, in the code example you gave it makes no sense at all.
Note that the definition of "I" was (likely) coded by one programmer and of WS-SUB by another (naming is different, VALUE clause is different for same purpose).
Programmer 2 looks like "old school": PIC S9(4), signed and taking up all the digits which "fit" in a half-word. The S9(9) is probably "far over the top" as per range of possible values, but such things concern Programmer 1 not at all.
Probably Programmer 2 had concerns about using an S9(9) COMP for something requiring (perhaps many) fewer than 9999 "things". "I'll be 'efficient' without changing the existing code". It seems to me unlikely that the field was ever defined as unsigned.
A COMP/COMP-4 with nine digits does have a performance penalty when used for calculations. Try "ADD 1" to a 9(9) and a 9(8) and a 9(10) and compare the generated code. If you can have nine digits, define with 9(10), otherwise 9(8), if you need a fullword.
Programmer 2 knows something of this.
The COMPUTE with + 0 is probably deliberate. Why did Programmer 2 use the COMPUTE like that (the original question)?
Now it is going to get complicated.
There are two "types" of "binary" fields on the Mainframe: those which will contain values limited by the PICture clause (USAGE BINARY, COMP and COMP-4); those which contain values limited by the field size (USAGE COMP-5).
With BINARY/COMP/COMP-4, the size of the field is determined from the PICture, and so are the values that can be held. PIC 9(4) is a halfword, with a maxiumum value of 9999. PIC S9(4) a halfword with values -9999 through +9999.
With COMP-5 (Native Binary), the PICture just determines the size of the field, all the bits of the field are relevant for the value of the field. PIC 9(1) to 9(4) define halfwords, pic 9(5) to 9(9) define fullwords, and 9(10) to 9(18) define doublewords. PIC 9(1) can hold a maximum of 65535, S9(1) -32,768 through +32,767.
All well and good. Then there is compiler option TRUNC. This has three options. STD, the default, BIN and OPT.
BIN can be considered to have the most far-reaching affect. BIN makes BINARY/COMP/COMP-4 behave like COMP-5. Everything becomes, in effect, COMP-5. PICtures for binary fields are ignored, except in determining the size of the field (and, curiously, with ON SIZE ERROR, which "errors" when the maxima according to the PICture are exceeded). Native Binary, in IBM Enterprise Cobol, generates, in the main, though not exclusively, the "slowest" code. Truncation is to field size (halfword, fullword, doubleword).
STD, the default, is "standard" truncation. This truncates to "PICture". It is therefore a "decimal" truncation.
OPT is for "performance". With OPT, the compiler truncates in whatever way is the most "performant" for a particular "code sequence". This can mean intermediate values and final values may have "bits set" which are "outside of the range" of the PICture. However, when used as a source, a binary field will always only reflect the value specified by the PICture, even if there are "excess" bits set.
It is important when using OPT that all binary fields "conform to PICture" meaning that code must never rely on bits which are set outside the PICture definition.
Note: Even though OPT has been used, the OPTimizer (OPT(STD) or OPT(FULL)) can still provide further optimisations.
This is all well and good.
However, a "pickle" can readily ensue if you "mix" TRUNC options, or if the binary definition in a CALLing program is not the same as in the CALLed program. The "mix" can occur if modules within the same run-unit are compiled with different TRUNC options, or if a binary field on a file is written with one TRUNC option and later read with another.
Now, I suspect Programmer 2 encountered something like this: Either, with TRUNC(OPT) they noticed "excess bits" in a field and thought there was a need to deal with them, or, through the "mix" of options in a run-unit or "across file usage" they noticed "excess bits" where there would be a need to do something about it (which was to "remove the mix").
Programmer 2 developed the COMPUTE A = B + 0 to "deal" with a particular problem (perceived or actual) and then applied it generally to their work.
This is a "guess", or, better, a "rationalisation" which works with the known information.
It is a "fake" fix. There was either no problem (the normal way that TRUNC(OPT) works) or the correct resolution was "normalisation" of the TRUNC option across modules/file use.
I do not want loads of people now rushing off and putting COMPUTE A = B + 0 in their code. For a start, they don't know why they are doing it. For a continuation it is the wrong thing to do.
Of course, do not just remove the "+ 0" from any of these that you find. If there is a "mix" of TRUNCs, a program may stop "working".
There is one situation in which I have used "ADD ZERO" for a BINARY/COMP/COMP-4. This is in a "Mickey Mouse" program, a program with no purpose but to try something out. Here I've used it as a method to "trick" the optimizer, as otherwise the optimizer could see unchanging values so would generate code to use literal results as all values were known at compile time. (A perhaps "neater" and more flexible way to do this which I picked up from PhilinOxford, is to use ACCEPT for the field). This is not the case, for certain, with the code in question.
I wonder if a testing version of the sources ever had
COMPUTE WS-SUB = I + 0
ON SIZE ERROR
DISPLAY "WS-SUB overflow"
STOP RUN
END-COMPUTE
with the range test discarded when the developer was satisfied and cleaning up? MOVE doesn't allow declarative SIZE statements. That's as much of a reason as I could see. Or perhaps developer habit of using COMPUTE to move, as a subtle reminder to question the need for defensive code at every step? And perhaps not knowing, as Joe pointed out, the SIZE clause would be just as effective without the + 0? Or a maintainer struggled with off by one errors and there was a corrective change from 1 to 0 after testing?