added support of slicing for IDSStructArray #20

prasad-sawantdesai · 2025-02-27T13:03:49Z

Added support of slicing for IDSStructArray

import imas

entry = imas.DBEntry("imas:mdsplus?user=public;pulse=116000;run=4;database=ITER_MD;version=3", "r")  
walids = entry.get("wall", autoconvert=False) # lazy=True
units = walids.description_2d[0].vessel.unit
print(units[8:])
print(units[0:100])
print(units[4:])
print(units[5])

maarten-ic · 2025-02-28T09:02:44Z

imas/ids_struct_array.py

+                if stop is None:
+                    stop = sys.maxsize
+
+                for i in range(start or 0, stop, step or 1):


Hi Prasad, Python slices are weird and have lots of edge cases with negative indices... the current logic doesn't quite capture that.

For example:

>>> import imas >>> entry = imas.DBEntry("imas:hdf5?path=./test", "w") 09:44:08 INFO Parsing data dictionary version 4.0.0 @dd_zip.py:166 >>> cp = entry.factory.core_profiles() >>> cp.profiles_1d.resize(10) >>> cp.ids_properties.homogeneous_time = 1 >>> cp.time = [*range(10)] 09:45:05 INFO Assigning incorrect type 'int64' to <IDSNumericArray (IDS:core_profiles, time, empty FLT_1D)>, attempting automatic conversion. @ids_primitive.py:483 >>> entry.put(cp) >>> cp.profiles_1d[:-5] [<IDSStructure (IDS:core_profiles, profiles_1d[0])>, <IDSStructure (IDS:core_profiles, profiles_1d[1])>, <IDSStructure (IDS:core_profiles, profiles_1d[2])>, <IDSStructure (IDS:core_profiles, profiles_1d[3])>, <IDSStructure (IDS:core_profiles, profiles_1d[4])>] >>> entry.get("core_profiles", lazy=True).profiles_1d[:-5] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/maarten/projects/iter-python/imas-python/imas/ids_struct_array.py", line 137, in __getitem__ return self.value[item] ~~~~~~~~~~^^^^^^ TypeError: 'NoneType' object is not subscriptable

Edge cases with negative indices:

Negative start, e.g. [-5:5], all items from the fifth from the end to the fifth from the beginning

Negative stop, e.g. [2:-2], all items from the third to the second-to-last

Negative increment, e.g. [::-1] all items in reverse order

What is the the use case for this feature? With a list comprehension users could capture (most) scenarios as well:

p1ds = [cp.profiles_1d[i] for i in range(2, 5)] # in reverse for p1d in reversed(cp.profiles_1d): ...

Thank you for reviewing @maarten-ic

Actually, this issue arises when using slicing for wall IDs, as shown below. There is a workaround—you can convert it into a list—but then you lose the IDSStructArray metadata. It would be convenient for users to work it as a list, what do you think @olivhoenen but of course we need to consider edge cases.
units = list(walids.description_2d[0].vessel.unit)

import imaspy as imas entry = imas.DBEntry("imas:mdsplus?user=public;pulse=116000;run=4;database=ITER_MD;version=3", "r") walids = entry.get("wall", autoconvert=False) units = walids.description_2d[0].vessel.unit # units = list(walids.description_2d[0].vessel.unit) workaround print(units[8:]) # 09:01:55 INFO Parsing data dictionary version 4.0.0 @dd_zip.py:166 # 09:01:59 INFO Parsing data dictionary version 3.40.0 @dd_zip.py:166 # Traceback (most recent call last): # File "/home/ITER/sawantp1/git/idstoolsimaspy/idstools/testbug.py", line 6, in <module> # print(units[8:]) # ~~~~~^^^^ # File "/work/imas/opt/EasyBuild/software/IMASPy/1.2.0-intel-2023b/lib/python3.11/site- # packages/imaspy/ids_struct_array.py", line 126, in __getitem__ # list_idx = int(item) ^^^^^^^^^ TypeError: int() argument must be a string, a bytes-like object or a real number, not 'slice'

Hi Prasad,

you can convert it into a list—but then you lose the IDSStructArray metadata

I don't understand the drawback: with the slicing you have implemented, unit[8:] is also a list, right?

when using slicing for wall IDs, as shown below

Yes, sure, but what's the actual use case for doing this? 🙂 I don't understand why a user would want to print all units except the first 8 (as you do in your code listing).

Note that I found out that slice objects have a method that give you the start/stop/step values for a sequence of given length: https://docs.python.org/3/reference/datamodel.html#slice.indices

This came up in the context of @prasad-sawantdesai work on IDStools, where different scripts are receiving IMAS URIs that may contain fragments (#ids:occ/ids_path) where the ids_path has slicing (as described in https://imas-data-dictionary.readthedocs.io/en/latest/_downloads/9e7ffd162c0237b61062528affd5fe2a/IDS-path-syntax.md).

What would be the easiest/recommended way to go from an ids_path string that contains slicing indices to an actual list of objects?

ps: in the case of the list of unit from the wall IDS, the machine description contains many different types of limiter and vessel units, not all of them make sense to overlay when plotting for example an equilibrium psi map

Hi Olivier,

where the ids_path has slicing

This PR doesn't really solve that case either. I could still not do wall.description_2d[0].vessel.unit[8:].element[:].name: the slice at unit[8:] will return a list that has no attribute element.

What would be the easiest/recommended way to go from an ids_path string that contains slicing indices to an actual list of objects?

This is actually a surprisingly tricky problem! And it mostly has to do with the possibility that IDSs don't have homogeneous array sizes deep down in the tree.

ibex has an implementation of this and, since it converts everything to JSON (which supports ragged arrays), it can avoid some of the difficulty. Looks like it is mostly implemented in _expand_single_path_element in this file. Though quickly scanning it, it looks like it doesn't handle the negative indices either (which is probably fine for the ibex use case).

I see two options for implementing your use case, with option 1 the easiest to implement and option 2 more generally useful 🙂

Add a method to IDSPath, for example IDSPath.goto_slices that returns a list of elements that match the slice syntax. It would be an extended form of IDSPath.goto (which returns a single element and raises a NotImplementedError when a slice is used in the path),

Implement slices on arrays of structures, which return a new object (e.g. IDSSlice). The IDSSlice can keep track of all objects that matched the slice expression, and allow further slicing of child elements, getting the matching elements, etc. That could look as follows:

>>> ids_slice = wall.description_2d[0].vessel.unit[8:] >>> ids_slice <IDSSlice (IDS:wall, description_2d[0].vessel.unit[8:], 4 matches)> >>> ids_slice.element <IDSSlice (IDS:wall, description_2d[0].vessel.unit[8:].element, 4 matches)> >>> ids_slice.element[:] <IDSSlice (IDS:wall, description_2d[0].vessel.unit[8:].element[:], 6 matches)> >>> ids_slice.element[:].name <IDSSlice (IDS:wall, description_2d[0].vessel.unit[8:].element[:].name, 6 matches)> >>> list(ids_slice.element[:].name) [<IDSString0D (IDS:wall, description_2d[0].vessel.unit[8].element[0].name)>, <IDSString0D (IDS:wall, description_2d[0].vessel.unit[8].element[1].name)>, <IDSString0D (IDS:wall, description_2d[0].vessel.unit[9].element[0].name)>, ... ]

In either case you'll need to decide how to handle edge cases. For example, what does it mean when you do unit[:2].element[2] when unit[0] has 4 elements and unit[1] has only 2 elements. Is this an IndexError? Or does this return a match of [unit[0].element[2]] and just ignore that there is no unit[1].element[2]?

There's probably more dragons hiding when implementing something like this -- there's a reason that it's not currently implemented in IDSPath 😉

I'm not sure why inhomogeneity is a problem there: if a user ask for a slice that does not exist we have an out-of-bound error, whether it is homogeneous or not (admittedly the risk increase in inhomogeneous case, but that should not be a concern for the implementation). IMO index-errors shall not be swallowed if they happen in nested elements, the error shall then just be propagated.

What do you think @prasad-sawantdesai, would something like 1 or 2 be useful in this case? 2 looks more appealing to me (but maybe that's because of the code snippet 🙄 ).

I will try to implement second option :)

…ct and added flatten and values functions

…-IDSStructArray

…prasad-sawantdesai/imas-python into feature/allow-slices-for-IDSStructArray

maarten-ic

Hi Prasad, I had a quick look at the current state of the PR.

Please have a look at below comments, I think it can simplify this logic a lot 🙂

imas/ids_slice.py

imas/ids_struct_array.py

SimonPinches · 2025-11-22T10:00:18Z

Do we want to squash all the commits with the same commit messages? (This PR now has > 3x the number of commits than files changed. Since this would involve a forced push this might not be very elegant for those who have cloned all branches so should we for the future move to only raising PRs from forks rather than pushing developments directly to this repo?)

maarten-ic · 2025-11-24T08:15:50Z

Do we want to squash all the commits with the same commit messages? (This PR now has > 3x the number of commits than files changed. Since this would involve a forced push this might not be very elegant for those who have cloned all branches so should we for the future move to only raising PRs from forks rather than pushing developments directly to this repo?)

Fine with me. This is done automatically when @olivhoenen presses the right buttons when merging, no force-push to this branch needed🙂
https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-commits

maarten-ic · 2025-11-24T09:26:53Z

Thanks @prasad-sawantdesai for addressing my previous feedback! I've had a quick go at using this and found the following things. Note that I have not (yet) reviewed the code another time, but I'll try to do that later this week. In the meanwhile, could you have a look at the following points?

Representation issue and inconsistencies with IDSSlice: name of first sliced AoS is missing; it would be nice to show the IDS name as well to make it consistent with other IDS object representations:

>>> eq.time_slice
<IDSStructArray (IDS:equilibrium, time_slice with 3 items)>
>>> eq.time_slice[:]
<IDSSlice ([:], 3 matches)>

Empty slices do not check if a getattr is valid:

>>> eq.time_slice[3:]
<IDSSlice ([3:], 0 matches)>
>>> eq.time_slice[3:].x  # This should still raise an exception, `x` is not a valid child node of time_slice.
<IDSSlice ([3:].x, 0 matches)>

The current getitem behaviour is confusing to me.
I would remove the behaviour for cp.profiles_1d[:].grid[0] and just raise an exception (it is also not possible to index cp.profiles_1d[0].grid[0]!). If a user wants to use the IDSSlice as if it is a list, they can just do list(cp.profiles_1d[:].grid)[0] or cp.profiles_1d[:].grid.values()[0], however I don't think this is a valid use case and people would just do cp.profiles_1d[0].grid instead.

>>> cp.profiles_1d[:].grid
<IDSSlice ([:].grid, 3 matches)>
>>> cp.profiles_1d[:].grid[0]  # Indexing an IDSSlice returns an IDSStructure
<IDSStructure (IDS:core_profiles, profiles_1d[0]/grid)>
>>> cp.profiles_1d[:].ion
<IDSSlice ([:].ion, 3 matches)>
>>> cp.profiles_1d[:].ion[0]  # Indexing an IDSSlice returns another IDSSlice (!)
<IDSSlice ([:].ion[0], 3 matches)>

…ation#20 (comment)

… if a getattr is valid-> iterorganization#20 (comment)

prasad-sawantdesai · 2025-11-29T22:44:17Z

Thanks @prasad-sawantdesai for addressing my previous feedback! I've had a quick go at using this and found the following things. Note that I have not (yet) reviewed the code another time, but I'll try to do that later this week. In the meanwhile, could you have a look at the following points?

Representation issue and inconsistencies with IDSSlice: name of first sliced AoS is missing; it would be nice to show the IDS name as well to make it consistent with other IDS object representations:
>>> eq.time_slice
<IDSStructArray (IDS:equilibrium, time_slice with 3 items)>
>>> eq.time_slice[:]
<IDSSlice ([:], 3 matches)>
Empty slices do not check if a getattr is valid:
>>> eq.time_slice[3:]
<IDSSlice ([3:], 0 matches)>
>>> eq.time_slice[3:].x  # This should still raise an exception, `x` is not a valid child node of time_slice.
<IDSSlice ([3:].x, 0 matches)>
The current getitem behaviour is confusing to me.
I would remove the behaviour for cp.profiles_1d[:].grid[0] and just raise an exception (it is also not possible to index cp.profiles_1d[0].grid[0]!). If a user wants to use the IDSSlice as if it is a list, they can just do list(cp.profiles_1d[:].grid)[0] or cp.profiles_1d[:].grid.values()[0], however I don't think this is a valid use case and people would just do cp.profiles_1d[0].grid instead.
>>> cp.profiles_1d[:].grid
<IDSSlice ([:].grid, 3 matches)>
>>> cp.profiles_1d[:].grid[0]  # Indexing an IDSSlice returns an IDSStructure
<IDSStructure (IDS:core_profiles, profiles_1d[0]/grid)>
>>> cp.profiles_1d[:].ion
<IDSSlice ([:].ion, 3 matches)>
>>> cp.profiles_1d[:].ion[0]  # Indexing an IDSSlice returns another IDSSlice (!)
<IDSSlice ([:].ion[0], 3 matches)>

Thank you for the review Maarten

Fixed the representation

>> eq.time_slice
<IDSStructArray (IDS:equilibrium, time_slice with 106 items)>
>> eq.time_slice[:]
<IDSSlice (IDS:equilibrium, time_slice[:] with 106 items)>

Raises an exception ( This should still raise an exception, x is not a valid child node of time_slice)

>> eq.time_slice[3:].x
Traceback (most recent call last):
  File "/home/ITER/sawantp1/github/IMAS-Python/representation.py", line 11, in <module>
    print(eq.time_slice[3:].x)
          ^^^^^^^^^^^^^^^^^^^
  File "/home/ITER/sawantp1/github/IMAS-Python/imas/ids_slice.py", line 219, in __getattr__
    child_elements = [getattr(element, name) for element in self]
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ITER/sawantp1/github/IMAS-Python/imas/ids_slice.py", line 219, in <listcomp>
    child_elements = [getattr(element, name) for element in self]
                      ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/ITER/sawantp1/github/IMAS-Python/imas/ids_structure.py", line 59, in __getattr__
    raise AttributeError(
AttributeError: IDS structure 'time_slice[3]' has no attribute 'x'

It retrieves the grid IDSStructure from all profiles_1d, and accessing the first element returns an IDSStructure

>>> cp.profiles_1d[1:3].grid
<IDSSlice (IDS:core_profiles, profiles_1d[1:3].grid with 2 items)>
>>> cp.profiles_1d[1:3].grid.shape
(2,)
>>> cp.profiles_1d[1:3].grid.values()
[<IDSStructure (IDS:core_profiles, profiles_1d[1]/grid)>, <IDSStructure (IDS:core_profiles, profiles_1d[2]/grid)>]
>>> cp.profiles_1d[1:3].grid.to_array()
array([<IDSStructure (IDS:core_profiles, profiles_1d[1]/grid)>,
       <IDSStructure (IDS:core_profiles, profiles_1d[2]/grid)>],
      dtype=object)
>>> cp.profiles_1d[1:3].grid[0]
<IDSStructure (IDS:core_profiles, profiles_1d[1]/grid)>

In the example below, cp.profiles_1d[1:3].ion[0] returns the first ion IDSStructure from all selected profiles_1d

>>> cp.profiles_1d[1:3].ion
<IDSSlice (IDS:core_profiles, profiles_1d[1:3].ion with 2 items)>
>>> cp.profiles_1d[1:3].ion.shape
(2, 3)
>>> cp.profiles_1d[1:3].ion.values()
[<IDSStructArray (IDS:core_profiles, profiles_1d[1]/ion with 3 items)>, <IDSStructArray (IDS:core_profiles, profiles_1d[2]/ion with 3 items)>]
>>> cp.profiles_1d[1:3].ion.to_array()
array([[<IDSStructure (IDS:core_profiles, profiles_1d[1]/ion[0])>,
        <IDSStructure (IDS:core_profiles, profiles_1d[1]/ion[1])>,
        <IDSStructure (IDS:core_profiles, profiles_1d[1]/ion[2])>],
       [<IDSStructure (IDS:core_profiles, profiles_1d[2]/ion[0])>,
        <IDSStructure (IDS:core_profiles, profiles_1d[2]/ion[1])>,
        <IDSStructure (IDS:core_profiles, profiles_1d[2]/ion[2])>]],
      dtype=object)
>>> cp.profiles_1d[1:3].ion[0]
<IDSSlice (IDS:core_profiles, profiles_1d[1:3].ion[0] with 2 items)>
>>> cp.profiles_1d[1:3].ion[0].to_array()
array([[<IDSStructure (IDS:core_profiles, profiles_1d[1]/ion[0])>],
       [<IDSStructure (IDS:core_profiles, profiles_1d[2]/ion[0])>]],
      dtype=object)
>>>

maarten-ic

Hi Prasad,

It retrieves the grid IDSStructure from all profiles_1d, and accessing the first element returns an IDSStructure
[...]
In the example below, cp.profiles_1d[1:3].ion[0] returns the first ion IDSStructure from all selected profiles_1d

Yes, I understand what it's doing, but I find it illogical and unexpected 😉
I would prefer to follow the principle of least astonishment, which - to me - would be: any operation on the IDSSlice should translate to the operation on the underlying IDS objects.

In pseudo code:

def do_something_with(ids_slice):
    return IDSSlice([do_something_with(ids_object) for ids_object in ids_slice])

We're doing this in most cases now (e.g. __getattr__, __getitem__ when the underlying objects are IDSStructArray) but not when the underlying objects are IDSStructure.

Let's set up a meeting to discuss in more detail if you want 🙂

(I still haven't reviewed the code in more detail, sorry! I'll do that this week.)

imas/ids_slice.py

imas/ids_struct_array.py

…comment)

…rganization#20 (comment)

…ed arrays. iterorganization#20 (comment)

…ith full path rather than slice path iterorganization#20 (comment)

…ganization#20 (comment)

…mment)

…ion#20 (review)

…-IDSStructArray

prasad-sawantdesai · 2026-01-06T08:40:20Z

Hi Prasad,

It retrieves the grid IDSStructure from all profiles_1d, and accessing the first element returns an IDSStructure
[...]
In the example below, cp.profiles_1d[1:3].ion[0] returns the first ion IDSStructure from all selected profiles_1d

Yes, I understand what it's doing, but I find it illogical and unexpected 😉 I would prefer to follow the principle of least astonishment, which - to me - would be: any operation on the IDSSlice should translate to the operation on the underlying IDS objects.

In pseudo code:
def do_something_with(ids_slice):
    return IDSSlice([do_something_with(ids_object) for ids_object in ids_slice])
We're doing this in most cases now (e.g. __getattr__, __getitem__ when the underlying objects are IDSStructArray) but not when the underlying objects are IDSStructure.

Let's set up a meeting to discuss in more detail if you want 🙂

(I still haven't reviewed the code in more detail, sorry! I'll do that this week.)

Right.. Updated here a3ca48c

added support of slicing for IDSStructArray

39d8a73

prasad-sawantdesai requested review from maarten-ic and olivhoenen February 27, 2025 13:03

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removed pull_request event

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prasad-sawantdesai added 12 commits November 3, 2025 09:20

merged with develop

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Merge branch 'develop' into feature/allow-slices-for-IDSStructArray

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added ids_slice.py and updated IDSStructArray to return IDSSlice obje…

7119a18

…ct and added flatten and values functions

added ids_slice.py and updated IDSStructArray to return IDSSlice obje…

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…ct and added flatten and values functions

removed flake8 issue

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Merge branch 'develop' into feature/allow-slices-for-IDSStructArray

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Fix per review comment iterorganization#20 (comment)

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Fix as per review comment iterorganization#20 (comment)

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Fix as per review comment iterorganization#20 (comment)

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Fix as per review comment iterorganization#20 (comment)

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Fix as per review comment iterorganization#20 (comment)

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Fix as per review comment iterorganization#20 (comment)

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Fix as per review comment iterorganization#20 (comment)

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Fix as per review comment iterorganization#20 (comment)

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Fix as per review comment iterorganization#20 (comment)

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lazy loaded objects supports slicing

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prasad-sawantdesai marked this pull request as ready for review November 21, 2025 23:02

prasad-sawantdesai added 6 commits November 24, 2025 17:19

fix representation issue and empty slice raises exception iterorganiz…

32265d1

…ation#20 (comment)

fix first and second point fix __repr__ and Empty slices do not check…

00752d2

… if a getattr is valid-> iterorganization#20 (comment)

fix first and second point fix __repr__ and Empty slices do not check…

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… if a getattr is valid-> iterorganization#20 (comment)

added tests

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fixed issues with to_array function

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raise value error when ragged arrays found iterorganization#20 (comment)

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Check if node is valid and return empty slice if array is empty itero…

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IDSSlice should have valid metadata, iterorganization#20 (comment)

d91d25b

the size of all items is not the same as the first, there may be ragg…

74e0d73

…ed arrays. iterorganization#20 (comment)

added property to get ids name in IDSMetadata class, build IDSSlice w…

16a608a

…ith full path rather than slice path iterorganization#20 (comment)

simplified values method according to suggestions from Maarten iteror…

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Simplified __getitem__ method for lazy lading iterorganization#20 (co…

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simplified to_array method iterorganization#20 (comment)

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fixed __getitem method principle of least astonishment, iterorganizat…

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prasad-sawantdesai marked this pull request as draft January 6, 2026 08:24

added support of slicing for IDSStructArray #20

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