fix(datagraph): iteration through edge_types wasnt updated for seg

[jjjermiah]

update edge_types to 8

handle new edge type for SEG->CT/MR mapping in final dataframe processing in parser

Summary by CodeRabbit

• New Features

  • Enhanced the DataGraph functionality to support an additional edge type, improving the representation of connections between different modalities.
  • Updated logic for edge handling and merging to accommodate the new edge type involving SEG and CT/MR.

• Bug Fixes

  • Corrected edge type handling in query processing to ensure accurate relationships in the resulting data.

• Chores

  • Updated package version to 1.5.7 and adjusted the dependency for attrs to allow broader version compatibility.

[coderabbitai]

Walkthrough

The changes involve modifications to the DataGraph class in src/imgtools/modules/datagraph.py, specifically enhancing the handling of edge types. The number of edge types has increased from 7 to 8, requiring updates to the _form_edges and _form_edge_study methods to accommodate this new edge type. Logic adjustments include new conditions for merging dataframes and handling queries related to the additional edge type, particularly involving the SEG modality. Additionally, the pyproject.toml file has been updated to reflect a new package version and a broader dependency constraint for attrs.

Changes

File Path	Change Summary
src/imgtools/modules/datagraph.py	Updated edge_types in _form_edges and _form_edge_study from np.arange(7) to np.arange(8). Enhanced logic for handling the new edge type, including new merge operations and query processing for SEG.
pyproject.toml	Updated package version to "1.5.7" and changed attrs dependency from ^23.2.0 to >=23.2.0.

Poem

In the land of data, where edges entwine,
A new type has blossomed, oh how it does shine!
With SEG now in play, connections expand,
Merging modalities, a grand data strand.
Hopping through queries, with joy we will sing,
For the DataGraph dances, oh what joy it brings! 🐇✨

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 6956dcc and bb519d3.

📒 Files selected for processing (1)

• pyproject.toml (1 hunks)

🔇 Additional comments (2)

pyproject.toml (2)

Line range hint 4-4: LGTM: Version bump to 1.5.7

The version increment is appropriate for a bug fix release addressing the edge_types iteration issue.

---

25-25: Verify compatibility with unrestricted attrs versions

The dependency constraint for attrs has been relaxed from ^23.2.0 to >=23.2.0, removing the upper version bound. While attrs has a good track record for backward compatibility, it's recommended to verify that the DataGraph functionality works correctly with the latest attrs version.

Let's check if there are any direct usages of attrs in the codebase that might be sensitive to version changes:

✅ Verification successful

Relaxing attrs version constraint is safe

Based on the codebase analysis, the usage of attrs is minimal and only involves basic Python attribute operations (hasattr, getattr) and HDF5 attributes (attrs). There are no direct uses of the attrs package decorators, classes, or functions that would be sensitive to version changes. The dependency is likely a transitive requirement, and the relaxed version constraint should not impact the functionality.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Search for attrs usage patterns in the codebase
# Expected: Find direct usage of attrs decorators or functions that might be version-sensitive

# Look for common attrs usage patterns
echo "Searching for attrs usage patterns..."
rg -l "import attr" || rg -l "from attr" || rg -l "@attr" || rg -l "import attrs" || rg -l "from attrs" || rg -l "@attrs"

Length of output: 199

---

Script:

#!/bin/bash
# Let's try a more comprehensive search for attrs usage
# Search for any Python files that might use attrs
echo "Searching for Python files..."
fd -e py -x cat {} | grep -i "attr" || true

# Also check if there are any test files that might be using attrs
echo -e "\nSearching specifically in test files..."
fd -e py "test_" -x cat {} | grep -i "attr" || true

# Look for any configuration or setup files that might reference attrs
echo -e "\nSearching in setup files..."
fd "setup.py|setup.cfg|pyproject.toml" -x cat {} | grep -i "attr" || true

Length of output: 2990

---

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[coderabbitai]

Actionable comments posted: 1

🧹 Outside diff range and nitpick comments (1)

src/imgtools/modules/datagraph.py (1)

317-333: Consider improving error messages for unsupported modality combinations.

When an unsupported modality combination is provided, the error message "Please enter the correct query" could be more helpful by listing the supported combinations, especially for the newly added SEG modality.

- raise ValueError("Please enter the correct query")
+ raise ValueError(
+     "Unsupported modality combination. Supported combinations:\n"
+     "- Single modality: CT, MR, RTSTRUCT, RTDOSE, PT, SEG\n"
+     "- Two modalities: CT/MR,SEG, CT/MR,RTSTRUCT, etc.\n"
+     "- Three or more: CT/MR,RTSTRUCT,RTDOSE, etc."
+ )

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between c9a10bb and 6956dcc.

📒 Files selected for processing (1)

• src/imgtools/modules/datagraph.py (2 hunks)

🔇 Additional comments (2)

src/imgtools/modules/datagraph.py (2)

317-333: LGTM: SEG modality handling is correctly implemented.

The implementation for handling SEG->CT/MR connections is consistent and properly renames the columns for the destination and origin nodes.

---

Line range hint 1-1: Verify SEG modality implementation consistency.

Let's verify that all SEG-related changes are consistent throughout the codebase.

✅ Verification successful

Based on the shell script results, I can now provide a final response regarding the SEG modality implementation consistency:

SEG modality implementation is properly integrated and consistent.

The codebase shows proper SEG modality support with consistent implementation:

• SEG modality is correctly handled in the loader system (src/imgtools/io/loaders.py) with a dedicated read_dicom_seg() function
• SEG reference handling is properly implemented in the crawler (src/imgtools/utils/crawl.py) with specific logic for SEG metadata extraction
• The implementation follows the same pattern as other modalities (CT, MR, RTSTRUCT, etc.)

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify SEG modality implementation consistency

# Test 1: Check for SEG modality references
echo "Checking SEG modality references..."
rg -l "SEG" --type py

# Test 2: Check for edge type 7 references
echo "Checking edge type 7 references..."
rg "edge.*7" --type py

# Test 3: Check for SEG in modality lists
echo "Checking SEG in modality lists..."
rg "supp_mods.*=.*\[.*\]" --type py

Length of output: 376

---

Script:

#!/bin/bash
# Let's get more context about SEG implementation

# Check SEG references with context
echo "SEG references with context:"
rg "SEG" --type py -B 2 -A 2

# Check modality-related configurations or lists
echo "Modality configurations:"
rg "modalities|MODALITIES|supported_mod" --type py -B 1 -A 1

# Check edge type definitions and handling
echo "Edge type handling:"
rg "edge_type|EDGE_TYPE" --type py -B 1 -A 1

# Check specific file content where SEG was found
echo "Content of files with SEG:"
cat src/imgtools/utils/crawl.py
echo "---"
cat src/imgtools/io/loaders.py

Length of output: 41039

[codecov]

Codecov Report

Attention: Patch coverage is 20.00000% with 4 lines in your changes missing coverage. Please review.

Project coverage is 45.73%. Comparing base (7abd175) to head (bb519d3).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/imgtools/modules/datagraph.py	20.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #131      +/-   ##
==========================================
+ Coverage   45.69%   45.73%   +0.04%     
==========================================
  Files          30       30              
  Lines        2867     2871       +4     
==========================================
+ Hits         1310     1313       +3     
- Misses       1557     1558       +1     

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