Vtk #944
Vtk #944
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📝 WalkthroughWalkthroughThe pull request introduces a new Python script in the Changes
Sequence DiagramsequenceDiagram
participant Input as HDF5 Input File
participant Converter as tovtk.py
participant Output as VTKHDF Output File
Input->>Converter: Read HDF5 File
Converter->>Converter: Extract Time Steps
Converter->>Converter: Process Magnetic Fields
Converter->>Converter: Process Electric Fields
Converter->>Output: Write Converted Data
The sequence diagram illustrates the high-level conversion process from HDF5 to VTKHDF, showing how the script reads the input file, processes magnetic and electric fields, and writes the converted data to the output file. ✨ Finishing Touches
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| AMRBoxOffsets = [] | ||
| dataOffsets = [] | ||
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| cellData_g = lvl.create_group("CellData") |
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Unused local variable Note
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| cellData_g = lvl.create_group("CellData") | ||
| pointData_g = lvl.create_group("PointData") | ||
| fieldData_g = lvl.create_group("FieldData") |
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Code scanning / CodeQL
Unused local variable Note
| cellData_g = lvl.create_group("CellData") | ||
| pointData_g = lvl.create_group("PointData") | ||
| fieldData_g = lvl.create_group("FieldData") | ||
| cellDataOffset_g = steps_lvl.create_group("CellDataOffset") |
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Code scanning / CodeQL
Unused local variable Note
| fieldData_g = lvl.create_group("FieldData") | ||
| cellDataOffset_g = steps_lvl.create_group("CellDataOffset") | ||
| pointDataOffset_g = steps_lvl.create_group("PointDataOffset") | ||
| FieldDataOffset_g = steps_lvl.create_group("FieldDataOffset") |
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Code scanning / CodeQL
Unused local variable Note
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Actionable comments posted: 2
🧹 Nitpick comments (4)
pyphare/pyphare/pharesee/tovtk.py (4)
11-43: Add detailed documentation for the Yee grid to primal conversion.The function performs complex averaging operations to convert from Yee grid to primal format. Consider adding:
- Docstring explaining the input parameters and return value
- Mathematical explanation of the averaging operations
- Documentation about the 2D to 3D conversion strategy
Here's a suggested docstring:
def BtoFlatPrimal(ph_bx, ph_by, ph_bz, npx, npy, npz, gn=2): + """Convert magnetic field components from Yee grid to flat primal format. + + Args: + ph_bx, ph_by, ph_bz: Magnetic field components on Yee grid + npx, npy, npz: Number of points in each dimension + gn: Number of ghost nodes (default=2) + + Returns: + numpy.ndarray: Flattened magnetic field in primal format (nbrPoints, 3) + """
45-77: Maintain documentation consistency with BtoFlatPrimal.The function has good inline comments but would benefit from the same level of documentation as suggested for BtoFlatPrimal.
Here's a suggested docstring:
def EtoFlatPrimal(ph_ex, ph_ey, ph_ez, npx, npy, npz, gn=2): + """Convert electric field components from Yee grid to flat primal format. + + Args: + ph_ex, ph_ey, ph_ez: Electric field components on Yee grid + npx, npy, npz: Number of points in each dimension + gn: Number of ghost nodes (default=2) + + Returns: + numpy.ndarray: Flattened electric field in primal format (nbrPoints, 3) + """
79-83: Remove hardcoded 2D assumption.The function hardcodes a 2D case by setting z-coordinates to 0. Consider making it dimension-agnostic for future extensibility.
def boxFromPatch(patch): + """Extract bounding box from patch attributes. + + Args: + patch: HDF5 group containing patch data + + Returns: + list: [x_min, x_max, y_min, y_max, z_min, z_max] + """ lower = patch.attrs["lower"] upper = patch.attrs["upper"] - return [lower[0], upper[0], lower[1], upper[1], 0, 0] # 2D + # Handle both 2D and 3D cases + z_min = lower[2] if len(lower) > 2 else 0 + z_max = upper[2] if len(upper) > 2 else 0 + return [lower[0], upper[0], lower[1], upper[1], z_min, z_max]
185-188: Optimize dictionary key check.Use
not inoperator directly on the dictionary instead of calling.keys().- if phare_lvl_name not in phare_h5["t"][time_str].keys(): + if phare_lvl_name not in phare_h5["t"][time_str]: print(f"no level {ilvl} at time {time}") continue🧰 Tools
🪛 Ruff (0.8.2)
185-185: Use
key not in dictinstead ofkey not in dict.keys()Remove
.keys()(SIM118)
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📒 Files selected for processing (1)
pyphare/pyphare/pharesee/tovtk.py(1 hunks)
🧰 Additional context used
🪛 Ruff (0.8.2)
pyphare/pyphare/pharesee/tovtk.py
163-163: Local variable cellData_g is assigned to but never used
Remove assignment to unused variable cellData_g
(F841)
165-165: Local variable fieldData_g is assigned to but never used
Remove assignment to unused variable fieldData_g
(F841)
166-166: Local variable cellDataOffset_g is assigned to but never used
Remove assignment to unused variable cellDataOffset_g
(F841)
168-168: Local variable FieldDataOffset_g is assigned to but never used
Remove assignment to unused variable FieldDataOffset_g
(F841)
185-185: Use key not in dict instead of key not in dict.keys()
Remove .keys()
(SIM118)
⏰ Context from checks skipped due to timeout of 90000ms (6)
- GitHub Check: build (macos-latest)
- GitHub Check: Analyze (cpp)
- GitHub Check: build (macos-14)
- GitHub Check: build (macos-13)
- GitHub Check: Analyze (python)
- GitHub Check: build (ubuntu-latest)
🔇 Additional comments (2)
pyphare/pyphare/pharesee/tovtk.py (2)
1-9: LGTM! Imports are appropriate.The necessary imports for HDF5 handling, numerical operations, and system operations are present.
85-91: Document the reason for adding 1 twice.The function adds 1 twice to each dimension when calculating the number of nodes. This needs explanation.
def nbrNodes(box): + """Calculate number of nodes in each dimension. + + Args: + box: List containing [x_min, x_max, y_min, y_max, z_min, z_max] + + Returns: + tuple: (npx, npy, npz) number of nodes in each dimension + """ lower = box[0], box[2], box[4] upper = box[1], box[3], box[5] + # Adding 1 for converting from cell count to node count + # and another 1 for including the end point npx = upper[0] - lower[0] + 1 + 1 npy = upper[1] - lower[1] + 1 + 1 npz = upper[2] - lower[2] + 1 + 1✅ Verification successful
Documentation accurately explains the double +1 addition
The double addition of 1 is correct and well-documented. The first +1 converts from cell count to node count (as there's always one more node than cells), and the second +1 ensures the endpoint is included, which is required for VTK format compatibility.
🏁 Scripts executed
The following scripts were executed for the analysis:
Error: No shell scripts found
Script:
#!/bin/bash # Search for usages of nbrNodes function rg "nbrNodes" -B 2 -A 2 # Search for similar grid calculations with double +1 pattern rg "([^+]\+\s*1\s*\+\s*1)" -B 2 -A 2 # Look for grid/mesh related files and documentation fd "grid|mesh" --type fLength of output: 3453
Script:
#!/bin/bash # Search for VTK-related code and documentation rg -g "*.py" -g "*.hpp" -g "*.cpp" "vtk|VTK" -B 2 -A 2 # Search for toFlatPrimal implementation rg "toFlatPrimal" -B 5 -A 5 # Search for any documentation about grid/node conversion rg -g "*.py" -g "*.md" "grid.*node|node.*grid" -B 2 -A 2Length of output: 4385
| cellData_g = lvl.create_group("CellData") | ||
| pointData_g = lvl.create_group("PointData") | ||
| fieldData_g = lvl.create_group("FieldData") | ||
| cellDataOffset_g = steps_lvl.create_group("CellDataOffset") | ||
| pointDataOffset_g = steps_lvl.create_group("PointDataOffset") | ||
| FieldDataOffset_g = steps_lvl.create_group("FieldDataOffset") | ||
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There was a problem hiding this comment.
🛠️ Refactor suggestion
Remove or document unused group variables.
Several group variables are created but never used: cellData_g, fieldData_g, cellDataOffset_g, and FieldDataOffset_g. Either remove them or document their intended future use.
- cellData_g = lvl.create_group("CellData")
pointData_g = lvl.create_group("PointData")
- fieldData_g = lvl.create_group("FieldData")
- cellDataOffset_g = steps_lvl.create_group("CellDataOffset")
pointDataOffset_g = steps_lvl.create_group("PointDataOffset")
- FieldDataOffset_g = steps_lvl.create_group("FieldDataOffset")📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| cellData_g = lvl.create_group("CellData") | |
| pointData_g = lvl.create_group("PointData") | |
| fieldData_g = lvl.create_group("FieldData") | |
| cellDataOffset_g = steps_lvl.create_group("CellDataOffset") | |
| pointDataOffset_g = steps_lvl.create_group("PointDataOffset") | |
| FieldDataOffset_g = steps_lvl.create_group("FieldDataOffset") | |
| pointData_g = lvl.create_group("PointData") | |
| pointDataOffset_g = steps_lvl.create_group("PointDataOffset") |
🧰 Tools
🪛 Ruff (0.8.2)
163-163: Local variable cellData_g is assigned to but never used
Remove assignment to unused variable cellData_g
(F841)
165-165: Local variable fieldData_g is assigned to but never used
Remove assignment to unused variable fieldData_g
(F841)
166-166: Local variable cellDataOffset_g is assigned to but never used
Remove assignment to unused variable cellDataOffset_g
(F841)
168-168: Local variable FieldDataOffset_g is assigned to but never used
Remove assignment to unused variable FieldDataOffset_g
(F841)
| def main(): | ||
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| path = sys.argv[1] | ||
| phare_h5 = h5py.File(path, "r") | ||
| times_str = list(phare_h5["t"].keys()) |
There was a problem hiding this comment.
Add error handling for command-line arguments.
The script assumes the input path is always provided and valid. Add proper error handling.
def main():
+ if len(sys.argv) != 2:
+ print("Usage: python tovtk.py <input_h5_file>")
+ sys.exit(1)
+
path = sys.argv[1]
+ if not os.path.exists(path):
+ print(f"Error: File {path} does not exist")
+ sys.exit(1)
+
phare_h5 = h5py.File(path, "r")📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def main(): | |
| path = sys.argv[1] | |
| phare_h5 = h5py.File(path, "r") | |
| times_str = list(phare_h5["t"].keys()) | |
| def main(): | |
| if len(sys.argv) != 2: | |
| print("Usage: python tovtk.py <input_h5_file>") | |
| sys.exit(1) | |
| path = sys.argv[1] | |
| if not os.path.exists(path): | |
| print(f"Error: File {path} does not exist") | |
| sys.exit(1) | |
| phare_h5 = h5py.File(path, "r") | |
| times_str = list(phare_h5["t"].keys()) |
| AMRBox.append(box) | ||
| nbr_boxes += 1 | ||
| npx, npy, npz = nbrNodes(box) | ||
| data = toFlatPrimal(ph_x, ph_y, ph_z, npx, npy, npz) |
Check failure
Code scanning / CodeQL
Potentially uninitialized local variable Error
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Actionable comments posted: 2
🧹 Nitpick comments (5)
pyphare/pyphare/pharesee/tovtk.py (5)
5-8: Add type hints and docstrings to improve code maintainability.Consider adding type hints and docstrings to all functions to improve code maintainability and IDE support. This will help other developers understand the expected input/output types and function purposes.
Example for the
BtoFlatPrimalfunction:-def BtoFlatPrimal(ph_bx, ph_by, ph_bz, npx, npy, npz, gn=2): +from typing import Tuple, ndarray + +def BtoFlatPrimal( + ph_bx: ndarray, + ph_by: ndarray, + ph_bz: ndarray, + npx: int, + npy: int, + npz: int, + gn: int = 2 +) -> ndarray: + """Convert magnetic field components from Yee grid to flat primal format. + + Args: + ph_bx: X-component of magnetic field on Yee grid + ph_by: Y-component of magnetic field on Yee grid + ph_bz: Z-component of magnetic field on Yee grid + npx: Number of points in X direction + npy: Number of points in Y direction + npz: Number of points in Z direction + gn: Number of ghost nodes (default: 2) + + Returns: + ndarray: Flattened magnetic field components in primal format + """Also applies to: 11-11, 45-45, 79-79, 85-85, 94-94
11-43: Consider refactoring field conversion functions to reduce code duplication.The
BtoFlatPrimalandEtoFlatPrimalfunctions share similar structure. Consider extracting common logic into a base function.Example refactor:
def _toFlatPrimal(components: dict, npx: int, npy: int, npz: int, gn: int = 2) -> ndarray: """Base function for converting field components to flat primal format. Args: components: Dictionary containing field components and their averaging rules npx, npy, npz: Number of points in each direction gn: Number of ghost nodes """ nbrPoints = npx * npy * npz result = np.zeros((nbrPoints, 3), dtype="f") # Create pure primal arrays primal = {k: np.zeros((npx, npy, npz), dtype=np.float32) for k in components} # Convert each component using its averaging rule for k, (data, rule) in components.items(): primal[k][:, :, 0] = rule(data, gn) primal[k][:, :, 1] = primal[k][:, :, 0] # Copy to z-dimension # Flatten to output format for i, k in enumerate(components): result[:, i] = primal[k].flatten(order="F") return resultAlso applies to: 45-77
21-32: Add detailed comments explaining the Yee grid to primal conversion process.The ghost node handling and averaging process in the dual direction needs better documentation. Also, document that this implementation assumes 2D data.
Add comments like:
# In Yee grid, B-field components are staggered: # Bx is defined at (i, j+1/2, k+1/2) # By is defined at (i+1/2, j, k+1/2) # Bz is defined at (i+1/2, j+1/2, k) # We average in the dual direction to get values at the primal grid pointsAlso applies to: 55-66
85-91: Document the node number calculation logic.The function adds 1 twice to each dimension. Add comments explaining why this is necessary (e.g., if it's related to cell-centered vs node-centered data).
def nbrNodes(box): + """Calculate number of nodes in each dimension. + + The +1 is added twice because: + 1. Convert from cell count to node count (+1) + 2. [Explain the second +1 here] + """
111-113: Use os.path.join for path construction.Replace string concatenation with
os.path.joinfor more robust path handling across different operating systems.- vtk_fn = f"{data_directory}/{phare_fn}.vtkhdf" + vtk_fn = os.path.join(data_directory, f"{phare_fn}.vtkhdf")
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Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
pyphare/pyphare/pharesee/tovtk.py(1 hunks)
🧰 Additional context used
🪛 Ruff (0.8.2)
pyphare/pyphare/pharesee/tovtk.py
163-163: Local variable cellData_g is assigned to but never used
Remove assignment to unused variable cellData_g
(F841)
165-165: Local variable fieldData_g is assigned to but never used
Remove assignment to unused variable fieldData_g
(F841)
166-166: Local variable cellDataOffset_g is assigned to but never used
Remove assignment to unused variable cellDataOffset_g
(F841)
168-168: Local variable FieldDataOffset_g is assigned to but never used
Remove assignment to unused variable FieldDataOffset_g
(F841)
185-185: Use key not in dict instead of key not in dict.keys()
Remove .keys()
(SIM118)
223-223: Undefined name b
(F821)
⏰ Context from checks skipped due to timeout of 90000ms (6)
- GitHub Check: build (macos-latest)
- GitHub Check: build (macos-14)
- GitHub Check: Analyze (cpp)
- GitHub Check: build (macos-13)
- GitHub Check: build (ubuntu-latest)
- GitHub Check: Analyze (python)
🔇 Additional comments (2)
pyphare/pyphare/pharesee/tovtk.py (2)
163-168: Remove unused group variables or document their future use.Several group variables are created but never used:
cellData_g,fieldData_g,cellDataOffset_g, andFieldDataOffset_g.🧰 Tools
🪛 Ruff (0.8.2)
163-163: Local variable
cellData_gis assigned to but never usedRemove assignment to unused variable
cellData_g(F841)
165-165: Local variable
fieldData_gis assigned to but never usedRemove assignment to unused variable
fieldData_g(F841)
166-166: Local variable
cellDataOffset_gis assigned to but never usedRemove assignment to unused variable
cellDataOffset_g(F841)
168-168: Local variable
FieldDataOffset_gis assigned to but never usedRemove assignment to unused variable
FieldDataOffset_g(F841)
94-97: Add error handling for command-line arguments.The script assumes the input path is always provided and valid.
| pointData_b[current_size:, :] = data | ||
| # pass | ||
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| current_size += b.shape[0] |
There was a problem hiding this comment.
Fix undefined variable reference.
Line 223 uses undefined variable b instead of data.
- current_size += b.shape[0]
+ current_size += data.shape[0]📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| current_size += b.shape[0] | |
| current_size += data.shape[0] |
🧰 Tools
🪛 Ruff (0.8.2)
223-223: Undefined name b
(F821)
| def boxFromPatch(patch): | ||
| lower = patch.attrs["lower"] | ||
| upper = patch.attrs["upper"] | ||
| return [lower[0], upper[0], lower[1], upper[1], 0, 0] # 2D | ||
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There was a problem hiding this comment.
💡 Codebase verification
Hardcoded 2D assumption in boxFromPatch needs to be fixed
The codebase has infrastructure for handling 3D data (as seen in core/box.py), but boxFromPatch in tovtk.py artificially limits functionality by hardcoding z=0. This should be modified to handle the z-dimension when present.
- Consider extracting z-coordinates from patch.attrs when available:
lower[2], upper[2] - Add dimension detection to support both 2D and 3D cases
🔗 Analysis chain
Validate 2D assumption in boxFromPatch function.
The function hardcodes z-dimension to 0, assuming 2D data. Consider validating this assumption or making it configurable for future 3D support.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if there are any 3D data files in the codebase
rg -l "upper\[2\]|lower\[2\]" --type py
Length of output: 167
Script:
#!/bin/bash
# Check Box class implementation and usage
ast-grep --pattern 'class Box' pyphare/pyphare/core/box.py
rg -A 5 "upper\[2\]|lower\[2\]" pyphare/pyphare/core/box.py
Length of output: 554
Just a quick and incomplete (just handles E and B) script to convert our data to vtkhdf and open it with paraview.
Just here as a way to learn paraview and decide whether it's a viable way for future diag formats.