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Separate dc parameter into two #91

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@sbaldu sbaldu commented Feb 21, 2025

This PR separates the dc parameter in two:

  • the usual one, now only used for the calculation of local density
  • a new one, seed_dc used in the kernel for finding clusters

github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 21, 2025
View reviewed changes
CLUEstering/CLUEstering.py
def __init__(self, dc_: float, rhoc_: float, dm_: [float, None] = None, ppbin: int = 10):
self.dc_ = dc_
def __init__(self, dc_: float, rhoc_: float, dm_: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):
self.dc = dc

Check warning

Code scanning / Pylintpython3 (reported by Codacy)

Attribute name "dc" doesn't conform to snake_case naming style Warning

Attribute name "dc" doesn't conform to snake_case naming style
CLUEstering/CLUEstering.py
@@ -258,13 +261,17 @@
self.elapsed_time = 0.

def set_params(self, dc: float, rhoc: float,
dm: [float, None], ppbin: int = 128) -> None:
self.dc_ = dc
dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128) -> None:

Check warning

Code scanning / Pylintpython3 (reported by Codacy)

Line too long (102/100) Warning

Line too long (102/100)
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 21, 2025
View reviewed changes
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 21, 2025
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include/CLUEstering/CLUE/CLUEAlpakaKernels.hpp
bool is_seed{(delta_i > d_c) && (rho_i >= rho_c)};
bool is_outlier{(delta_i > dm) && (rho_i < rho_c)};
bool is_seed{(delta_i > seed_dc) && (rho_i >= rhoc)};
bool is_outlier{(delta_i > dm) && (rho_i < rhoc)};

Check warning

Code scanning / Cppcheck (reported by Codacy)

The scope of the variable 'is_outlier' can be reduced. Warning

The scope of the variable 'is_outlier' can be reduced.
include/CLUEstering/CLUEstering.hpp
@@ -24,17 +24,26 @@
template <uint8_t Ndim>
class CLUEAlgoAlpaka {
public:
explicit CLUEAlgoAlpaka(float dc, float rhoc, float dm, int pPBin, Queue queue)
: dc_{dc}, rhoc_{rhoc}, dm_{dm}, pointsPerTile_{pPBin} {
explicit CLUEAlgoAlpaka(

Check notice

Code scanning / Cppcheck (reported by Codacy)

Member variable 'CLUEAlgoAlpaka::m_tiles' is not initialized in the constructor. Note

Member variable 'CLUEAlgoAlpaka::m_tiles' is not initialized in the constructor.
include/CLUEstering/CLUEstering.hpp
explicit CLUEAlgoAlpaka(float dc, float rhoc, float dm, int pPBin, Queue queue)
: dc_{dc}, rhoc_{rhoc}, dm_{dm}, pointsPerTile_{pPBin} {
explicit CLUEAlgoAlpaka(
float dc, float rhoc, float dm, int pPBin, Queue queue, float seed_dc = -1.f)

Check notice

Code scanning / Cppcheck (reported by Codacy)

MISRA 17.8 rule Note

MISRA 17.8 rule
include/CLUEstering/CLUEstering.hpp
TilesAlpaka<Ndim>* tile_buffer)
: dc_{dc}, rhoc_{rhoc}, dm_{dm}, pointsPerTile_{pPBin} {
TilesAlpaka<Ndim>* tile_buffer,
float seed_dc = -1.f)

Check notice

Code scanning / Cppcheck (reported by Codacy)

MISRA 17.8 rule Note

MISRA 17.8 rule
include/CLUEstering/CLUEstering.hpp
TilesAlpaka<Ndim>* tile_buffer,
float seed_dc = -1.f)

: m_dc{dc}, m_seed_dc{seed_dc}, m_rhoc{rhoc}, m_dm{dm}, m_pointsPerTile{pPBin} {

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Code scanning / Cppcheck (reported by Codacy)

MISRA 12.3 rule Note

MISRA 12.3 rule
include/CLUEstering/CLUEstering.hpp
d_followers =
clue::make_device_buffer<VecArray<int32_t, max_followers>[]>(queue_, reserve);
clue::make_device_buffer<VecArray<int32_t, max_followers>[]>(queue, reserve);

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Code scanning / Cppcheck (reported by Codacy)

MISRA 12.3 rule Note

MISRA 12.3 rule
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 21, 2025
View reviewed changes
CLUEstering/CLUEstering.py
def __init__(self, dc_: float, rhoc_: float, dm_: [float, None] = None, ppbin: int = 10):
self.dc_ = dc_
def __init__(self, dc_: float, rhoc_: float, dm_: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):
self.dc = dc

Check warning

Code scanning / Pylint (reported by Codacy)

Attribute name "dc" doesn't conform to snake_case naming style Warning

Attribute name "dc" doesn't conform to snake_case naming style
CLUEstering/CLUEstering.py
@@ -258,13 +261,17 @@
self.elapsed_time = 0.

def set_params(self, dc: float, rhoc: float,
dm: [float, None], ppbin: int = 128) -> None:
self.dc_ = dc
dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128) -> None:

Check warning

Code scanning / Pylint (reported by Codacy)

Line too long (102/100) Warning

Line too long (102/100)
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 24, 2025
View reviewed changes
CLUEstering/CLUEstering.py
@@ -675,32 +682,32 @@

start = time.time_ns()
if backend == "cpu serial":
cluster_id_is_seed = cpu_serial.mainRun(self.dc_, self.rhoc, self.dm, self.ppbin,
data.coords, data.results,
cluster_id_is_seed = cpu_serial.mainRun(self.dc, self.rhoc, self.dm, self.seed_dc,

Check warning

Code scanning / Prospector (reported by Codacy)

Unused variable 'cluster_id_is_seed' (unused-variable) Warning

Unused variable 'cluster_id_is_seed' (unused-variable)
CLUEstering/CLUEstering.py
self.kernel, data.n_dim,
data.n_points, block_size, device_id)
else:
print("CUDA module not found. Please re-compile the library and try again.")

elif backend == "gpu hip":
if hip_found:
cluster_id_is_seed = gpu_hip.mainRun(self.dc_, self.rhoc, self.dm, self.ppbin,
data.coords, data.results,
cluster_id_is_seed = gpu_hip.mainRun(self.dc, self.rhoc, self.dm, self.seed_dc,

Check warning

Code scanning / Prospector (reported by Codacy)

local variable 'cluster_id_is_seed' is assigned to but never used (F841) Warning

local variable 'cluster_id_is_seed' is assigned to but never used (F841)
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 24, 2025
View reviewed changes
CLUEstering/CLUEstering.py
@@ -675,32 +682,32 @@

start = time.time_ns()
if backend == "cpu serial":
cluster_id_is_seed = cpu_serial.mainRun(self.dc_, self.rhoc, self.dm, self.ppbin,
data.coords, data.results,
cluster_id_is_seed = cpu_serial.mainRun(self.dc, self.rhoc, self.dm, self.seed_dc,

Check notice

Code scanning / Pylintpython3 (reported by Codacy)

Unused variable 'cluster_id_is_seed' Note

Unused variable 'cluster_id_is_seed'
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 24, 2025
View reviewed changes
CLUEstering/CLUEstering.py
@@ -675,32 +682,32 @@

start = time.time_ns()
if backend == "cpu serial":
cluster_id_is_seed = cpu_serial.mainRun(self.dc_, self.rhoc, self.dm, self.ppbin,
data.coords, data.results,
cluster_id_is_seed = cpu_serial.mainRun(self.dc, self.rhoc, self.dm, self.seed_dc,

Check notice

Code scanning / Pylint (reported by Codacy)

Unused variable 'cluster_id_is_seed' Note

Unused variable 'cluster_id_is_seed'
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 24, 2025
View reviewed changes
CLUEstering/CLUEstering.py
self.dm = dm_
if dm_ is None:
self.dm = dc_
def __init__(self, dc: float, rhoc: float, dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):

Check warning

Code scanning / Prospector (reported by Codacy)

Too many arguments (6/5) (too-many-arguments) Warning

Too many arguments (6/5) (too-many-arguments)
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 24, 2025
View reviewed changes
CLUEstering/CLUEstering.py
self.dm = dm_
if dm_ is None:
self.dm = dc_
def __init__(self, dc: float, rhoc: float, dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):

Check warning

Code scanning / Pylintpython3 (reported by Codacy)

Too many arguments (6/5) Warning

Too many arguments (6/5)
CLUEstering/CLUEstering.py
self.dm = dm_
if dm_ is None:
self.dm = dc_
def __init__(self, dc: float, rhoc: float, dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):

Check warning

Code scanning / Pylintpython3 (reported by Codacy)

Line too long (122/100) Warning

Line too long (122/100)
CLUEstering/CLUEstering.py
def __init__(self, dc: float, rhoc: float, dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):
self.dc = dc
self.rhoc = rhoc
self.dm = dm

Check warning

Code scanning / Pylintpython3 (reported by Codacy)

Attribute name "dm" doesn't conform to snake_case naming style Warning

Attribute name "dm" doesn't conform to snake_case naming style
github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 24, 2025
View reviewed changes
CLUEstering/CLUEstering.py
self.dm = dm_
if dm_ is None:
self.dm = dc_
def __init__(self, dc: float, rhoc: float, dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):

Check warning

Code scanning / Pylint (reported by Codacy)

Too many arguments (6/5) Warning

Too many arguments (6/5)
CLUEstering/CLUEstering.py
self.dm = dm_
if dm_ is None:
self.dm = dc_
def __init__(self, dc: float, rhoc: float, dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):

Check warning

Code scanning / Pylint (reported by Codacy)

Line too long (122/100) Warning

Line too long (122/100)
CLUEstering/CLUEstering.py
def __init__(self, dc: float, rhoc: float, dm: [float, None] = None, seed_dc: [float, None] = None, ppbin: int = 128):
self.dc = dc
self.rhoc = rhoc
self.dm = dm

Check warning

Code scanning / Pylint (reported by Codacy)

Attribute name "dm" doesn't conform to snake_case naming style Warning

Attribute name "dm" doesn't conform to snake_case naming style
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@sbaldu