zeiss / czicheck Goto Github PK

Is your feature request related to a problem? Please describe.
Beyond conformity to schema, there are semantic checks on the data like "uniqueness of IDs" which should be done.

Describe the solution you'd like
Where the semantic requires unique Ids, it should be checked that the Id-attribute is unique. Here is an example of a malformed XML:

Describe alternatives you've considered
Expressing this condition in the XML-schema - not sure if that's possible.

czicheck is a very valuable tool to check & verify the integrity of a CZI image in various situations, but can be currently only used directly from the command line. Therefore it would be beneficial to have:

• python wrapper for czichecker
• can be used directly from python
• maybe as part of pylibCZIrw?

For CZIs containing compressed data, it would be beneficial to have a checker which actually decodes the data (and thereby checks for the correctness of the compressed data). In addition, consistency checks like "whether size and pixeltype (esp. in case of JPGXR) matches the CZI-level-description" should be done.

libCZI recently gained functionality to access CZIs via http/https-protocol.

This functionality should be made available in CZICheck.

A new command-line switch should be added to CZICheck allowing to specifiy the reader - c.f. CZICmd and the option "--source-stream-class".

A checker should validate that the redundant information in subblock-directory and subblock itself is consistent. Wrt to the subblock-directory, this would be this information which is expected to be equal to the corresponding information in the subblock itself.

Is your feature request related to a problem? Please describe.
CziCheck does currently not warn or report an error for subblocks with physical > 1 (for dimensions other than X,Y,M).
libCzi has been extended to throw an exception if strict parsing is used.

Describe the solution you'd like
Add a "boolean" command line argument "-l/--laxparsing" which enables the activation of strict parsing.

In order to integrate CZICheck in automatic workflows, it seems beneficial to have an output of the check in a machine-readable format.

E.g. it would be nice to have an option that the check-result is output in Json, XML or CVS format, which can then be easily parsed and interpreted.

Suggestion: consider libxo for implementing the desired fucntionality

CZIs can contain topology data, and there is specific metadata describing this kind of data.
Idea is to have a checker dedicated validating the semantic of the topology metadata.

This checker should include at least:

• do the referenced channels exist
• do the referenced channels have the appropriate pixel type
• is there no superfluous additional data given within the TopographyDataItems-XML-nodes
• is "StartC" attribute present