Doubt about future phases (and bugs found - which are not being caught by tests)

[Devguru-codes]

Hello @ltorres6 sir, I just wanted to know if I can contribute and help with the completion of phase 3. I can contribute in its completion.

Also when I was traversing the project and seeing the phase 3 tasks - I have found 2 bugs.
Bug 1 - Missing affine in _compute_t1_map() - osipy\pipeline\dce_pipeline.py (line 278)
we need affine here because when a user calls DCEPipeline.run() with a raw numpy array for t1_data instead of a pre-built PerfusionDataset it will raise an TypeError: PerfusionDataset.init() missing 1 required positional argument: 'affine'.The population AIF path is unaffected here.
What is needed - if we add just a line - affine=np.eye(4) - this will fix the bug completely.
Code to reproduce the bug -

import numpy as np
import traceback
print("BUG 1: Missing affine in _compute_t1_map()")
try:
    from osipy.pipeline.dce_pipeline import DCEPipeline, DCEPipelineConfig

    # Create a pipeline that needs T1 mapping
    config = DCEPipelineConfig(
        t1_mapping_method="vfa",
        model="extended_tofts",
    )
    pipeline = DCEPipeline(config)

    # Create fake data
    dce_signal = np.random.rand(4, 4, 2, 10).astype(np.float32)
    time = np.linspace(0, 5, 10).astype(np.float32)
    flip_angles = np.array([2.0, 5.0, 10.0, 15.0])
    tr = 5.0

    # Pass t1_data as a RAW NDARRAY (not PerfusionDataset)
    # This is what triggers the bug at line 278
    t1_raw_array = np.random.rand(4, 4, 2, 4).astype(np.float32)

    print("Calling: pipeline._compute_t1_map(t1_raw_array, flip_angles, tr)")
    print()
    result = pipeline._compute_t1_map(t1_raw_array, flip_angles, tr)
    print("UNEXPECTED: No error raised!")

except TypeError as e:
    print(f"CRASH - TypeError: {e}")
    print()
    print("Root cause: PerfusionDataset.__init__() is missing required")
    print("argument 'affine'. The dataclass requires it but dce_pipeline.py")
    print("line 278 doesn't pass it.")
    print()
    traceback.print_exc()
except Exception as e:
    print(f"CRASH - {type(e).__name__}: {e}")
    print()
    traceback.print_exc()

Proof - terminal screenshot -

Bug 2 - Wrong kwarg time and need affine in _get_aif()- osipy\pipeline\dce_pipeline.py (lines 308 to 312)
time is not a valid field. PerfusionDataset dataclass has field name is time_points.
affine is also required here
why is the issue not caught - when a user configures aif_source: detect in their YAML config (to auto-detect AIF from data). The default aif_source: population is unaffected, which is why tests pass - no test exercises this exact code path.
What to change - Change time=time to time_points=time and add affine=np.eye(4).
Code to reproduce the bug -

import numpy as np
import traceback
print("BUG 2: Wrong kwarg name in _get_aif()")
print("Trigger: Set aif_source='detect' and call _get_aif()")
print()

try:
    from osipy.pipeline.dce_pipeline import DCEPipeline, DCEPipelineConfig

    # Create a pipeline with AIF detection enabled
    config = DCEPipelineConfig(
        aif_source="detect",  # <-- This triggers the buggy code path
        model="extended_tofts",
    )
    pipeline = DCEPipeline(config)

    # Create fake 4D concentration data
    concentration = np.random.rand(4, 4, 2, 10).astype(np.float32)
    time = np.linspace(0, 5, 10).astype(np.float32)
    mask = np.ones((4, 4, 2), dtype=bool)

    print("Calling: pipeline._get_aif(concentration, time, mask)")
    print()
    print("This code at line 308-312 does:")
    print("  PerfusionDataset(data=concentration, modality=..., time=time)")
    print()
    print("Problem 1: 'time' is not a valid field (should be 'time_points')")
    print("Problem 2: 'affine' is missing (required field)")
    print()

    result = pipeline._get_aif(concentration, time, mask)
    print("UNEXPECTED: No error raised!")

except TypeError as e:
    print(f"CRASH - TypeError: {e}")
    print()
    print("Root cause: PerfusionDataset() got unexpected keyword 'time'")
    print("AND is missing required keyword 'affine'.")
    print()
    traceback.print_exc()
except Exception as e:
    print(f"CRASH - {type(e).__name__}: {e}")
    print()
    traceback.print_exc()

print()
print("CONCLUSION: Both bugs are real and cause crashes.")

Proof - ss from terminal -

@ltorres6 sir, I want to discuss about the issues before I create the issue and submit the fix for it. Also wanted to contribute in phase 3. Thank you sir.

[Devguru-codes]

Also we should add that in tests.