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Merged
Linked-Liszt merged 6 commits into from
Dec 8, 2025
Merged

Input Form Polish #82

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79235d6
Set new max_peaks value and handle blank field
Linked-Liszt Dec 6, 2025
d857919
test: Add second test log of scan data into automated tests
Linked-Liszt Dec 6, 2025
59b1830
Feat: Add Jon's HKL parsing to form
Linked-Liszt Dec 8, 2025
18ef1b8
refactor: Move srange into package & utilities folder
Linked-Liszt Dec 8, 2025
5ef5537
feat: Add absolute path resolution for non-root path inputs
Linked-Liszt Dec 8, 2025
73ebfb1
test: Fix expected name after removing names from logs
Linked-Liszt Dec 8, 2025
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21 changes: 4 additions & 17 deletions laue_portal/components/peakindex_form.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -146,13 +146,13 @@
dbc.Row(
[
dbc.Col(
_field("Geometry File", "geoFile", size='md',
_field("Geometry File", "geoFile",
kwargs={
"type": "text",
"placeholder": "",
}),
className="flex-grow-1",
style={"minWidth": 150},
style={"minWidth": 0},
),
dbc.Col(
dbc.Row(
Expand Down Expand Up @@ -191,6 +191,7 @@
className="g-2 justify-content-end", # g-2 adds a nice gap
),
xs=12, md="auto", # whole block drops under input on small screens
className="mb-3", # fixes y alignment
),
],
className="mb-3 g-2",
Expand Down Expand Up @@ -410,7 +411,7 @@
# _field("Index K", "indexK", size='md'),
# _field("Index L", "indexL", size='md'),
_field("Cone Angle [deg]", "indexCone", size='md'),
_field("Max no. of Spots (empty for all)", "max_peaks", size='md'),
_field("Max no. of Spots (empty: 200)", "max_peaks", size='md'),
]
),
_stack(
Expand All @@ -419,20 +420,6 @@

]
),
# dbc.Button(
# "Show Path to Program",
# id="collapse2-button",
# className="mb-3",
# color="primary",
# n_clicks=0,
# ),
# dbc.Collapse(
# [
# _field("Indexing Path", "indexingPath"),
# ],
# id="collapse2",
# is_open=False,
# ),
],
title="Indexing Parameters",
item_id = "item-3",
Expand Down
2 changes: 1 addition & 1 deletion laue_portal/pages/callback_registrars.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
import laue_portal.database.session_utils as session_utils
from laue_portal.database.db_utils import get_data_from_id, parse_parameter, parse_IDnumber
from laue_portal.config import DEFAULT_VARIABLES, VALID_HDF_EXTENSIONS
from srange import srange
from laue_portal.utilities.srange import srange

logger = logging.getLogger(__name__)

Expand Down
126 changes: 92 additions & 34 deletions laue_portal/pages/create_peakindexing.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,13 +35,38 @@
register_check_filenames_callback,
_merge_field_values
)
from srange import srange
from laue_portal.utilities.srange import srange
import laue_portal.database.session_utils as session_utils
from laue_portal.utilities.hkl_parse import str2hkl

logger = logging.getLogger(__name__)


def build_output_folder_template(scan_num_int, data_path,
def resolve_path_with_root(path, root_path):
"""
Resolve a path, using root_path only if the path is relative.
If path is absolute, return it as-is (overriding root_path).

Args:
path: The path to resolve (can be relative or absolute)
root_path: The root path to prepend if path is relative

Returns:
str: The resolved full path
"""
if not path:
return ""

# Check if path is absolute
if os.path.isabs(path):
# Path is absolute - use it directly, ignore root_path
return path
else:
# Path is relative - combine with root_path
return os.path.join(root_path, path.lstrip('/'))


def build_output_folder_template(scan_num_int, data_path,
wirerecon_id_int=None, recon_id_int=None):
"""
Build output folder template based on available IDs from database chain.
Expand Down Expand Up @@ -108,7 +133,7 @@ def build_output_folder_template(scan_num_int, data_path,
"detectorCropY1": 0,
"detectorCropY2": 2047,
"min_size": 3, #1.13
"max_peaks": 50,
"max_peaks": 200,
"smooth": False, #0
"maskFile": "None",
"indexKeVmaxCalc": 17.2, #17.2
Expand Down Expand Up @@ -140,11 +165,6 @@ def build_output_folder_template(scan_num_int, data_path,
"filenamePrefix": "HAs_long_laue1_",
}

# DEFAULT_VARIABLES = {
# "author": "",
# "notes": "",
# }

dash.register_page(__name__)

layout = dbc.Container(
Expand Down Expand Up @@ -358,6 +378,7 @@ def validate_peakindexing_inputs(ctx):
'depthRange',
'threshold',
'thresholdRatio',
'max_peaks',
'scanNumber',
'wirerecon_id',
'recon_id',
Expand Down Expand Up @@ -564,11 +585,18 @@ def validate_field(field_name, **kwargs):
custom_message="Recon ID is not a valid integer"
)

# 2. Check if data files exist for this input (skip if root_path or data_path invalid)
if 'root_path' not in validation_result['errors'] and 'data_path' not in validation_result['errors']:
# 2. Check if data files exist for this input (skip if root_path invalid)
if 'root_path' not in validation_result['errors']:
current_data_path = validate_field('data_path')
if current_data_path is not None:
current_full_data_path = os.path.join(root_path, current_data_path.lstrip('/'))
# Warn if absolute path is being used (root_path will be ignored)
if os.path.isabs(current_data_path):
add_validation_message(
validation_result, 'warnings', 'data_path', input_prefix,
custom_message="Data Path is absolute - Root Path will be ignored"
)

current_full_data_path = resolve_path_with_root(current_data_path, root_path)

# Check if directory exists
if not os.path.exists(current_full_data_path):
Expand Down Expand Up @@ -765,8 +793,15 @@ def validate_field(field_name, **kwargs):
current_outputFolder = validate_field('outputFolder', display_name="Output Folder")
if current_outputFolder is not None:
if 'root_path' not in validation_result['errors']:
# Warn if absolute path is being used (root_path will be ignored)
if os.path.isabs(current_outputFolder):
add_validation_message(
validation_result, 'warnings', 'outputFolder', input_prefix,
custom_message="Output Folder is absolute - Root Path will be ignored"
)

if '%d' not in current_outputFolder:
full_output_path = os.path.join(root_path, current_outputFolder.lstrip('/'))
full_output_path = resolve_path_with_root(current_outputFolder, root_path)
if os.path.exists(full_output_path):
add_validation_message(validation_result, 'warnings', 'outputFolder', input_prefix,
custom_message="Output Folder already exists")
Expand All @@ -775,7 +810,14 @@ def validate_field(field_name, **kwargs):
current_geoFile = validate_field('geoFile', display_name="Geometry File")
if current_geoFile is not None:
if 'root_path' not in validation_result['errors']:
full_geo_path = os.path.join(root_path, current_geoFile.lstrip('/'))
# Warn if absolute path is being used (root_path will be ignored)
if os.path.isabs(current_geoFile):
add_validation_message(
validation_result, 'warnings', 'geoFile', input_prefix,
custom_message="Geometry File is absolute - Root Path will be ignored"
)

full_geo_path = resolve_path_with_root(current_geoFile, root_path)
if not os.path.exists(full_geo_path):
add_validation_message(validation_result, 'errors', 'geoFile', input_prefix,
custom_message="Geometry File not found")
Expand All @@ -784,7 +826,14 @@ def validate_field(field_name, **kwargs):
current_crystFile = validate_field('crystFile', display_name="Crystal File")
if current_crystFile is not None:
if 'root_path' not in validation_result['errors']:
full_cryst_path = os.path.join(root_path, current_crystFile.lstrip('/'))
# Warn if absolute path is being used (root_path will be ignored)
if os.path.isabs(current_crystFile):
add_validation_message(
validation_result, 'warnings', 'crystFile', input_prefix,
custom_message="Crystal File is absolute - Root Path will be ignored"
)

full_cryst_path = resolve_path_with_root(current_crystFile, root_path)
if not os.path.exists(full_cryst_path):
add_validation_message(validation_result, 'errors', 'crystFile', input_prefix,
custom_message="Crystal File not found")
Expand Down Expand Up @@ -885,20 +934,15 @@ def validate_field(field_name, **kwargs):
add_validation_message(validation_result, 'errors', 'indexCone', input_prefix,
custom_message="Index Cone must be between 0 and 180 degrees")

# 8. Validate indexHKL for this input
# 8. Validate indexHKL for this input using str2hkl
if 'indexHKL' not in validation_result['errors']:
current_indexHKL = str(parsed_fields['indexHKL'][i])
if len(current_indexHKL) != 3:
current_indexHKL_str = str(parsed_fields['indexHKL'][i])
try:
hkl_values = str2hkl(current_indexHKL_str, Nmin=3, Nmax=3)
# Validation successful - hkl_values is a list of 3 integers or floats
except (TypeError, ValueError) as e:
add_validation_message(validation_result, 'errors', 'indexHKL', input_prefix,
custom_message="Index HKL must be 3 digits (e.g., '001')")
else:
try:
int(current_indexHKL[0])
int(current_indexHKL[1])
int(current_indexHKL[2])
except ValueError:
add_validation_message(validation_result, 'errors', 'indexHKL', input_prefix,
custom_message="Index HKL must contain only digits")
custom_message=f"Index HKL parsing error: {str(e)}")


# Add successes for fields that passed all validations
Expand Down Expand Up @@ -1192,6 +1236,9 @@ def submit_parameters(n,
detectorCropY1_list = parse_parameter(PEAKINDEX_DEFAULTS["detectorCropY1"], num_inputs)
detectorCropY2_list = parse_parameter(PEAKINDEX_DEFAULTS["detectorCropY2"], num_inputs)
min_size_list = parse_parameter(min_size, num_inputs)
# Auto-fill max_peaks with default value of 200 if empty
if not max_peaks or max_peaks == '':
max_peaks = str(PEAKINDEX_DEFAULTS["max_peaks"])
max_peaks_list = parse_parameter(max_peaks, num_inputs)
smooth_list = parse_parameter(smooth, num_inputs)
maskFile_list = parse_parameter(maskFile, num_inputs)
Expand Down Expand Up @@ -1352,8 +1399,19 @@ def submit_parameters(n,
session.add(subjob)
subjob_count += 1

# Extract HKL values from indexHKL parameter
current_indexHKL = str(indexHKL_list[i])
# Extract HKL values from indexHKL parameter using str2hkl
current_indexHKL_str = str(indexHKL_list[i])
try:
hkl_values = str2hkl(current_indexHKL_str, Nmin=3, Nmax=3)
# hkl_values is a list of 3 integers or floats [h, k, l]
except (TypeError, ValueError) as e:
logger.error(f"Failed to parse HKL '{current_indexHKL_str}': {e}")
set_props("alert-submit", {
'is_open': True,
'children': f'Invalid HKL value: {current_indexHKL_str}',
'color': 'danger'
})
continue

# Get filefolder and filenamePrefix
current_data_path = data_path_list[i]
Expand Down Expand Up @@ -1399,9 +1457,9 @@ def submit_parameters(n,
indexKeVmaxCalc=indexKeVmaxCalc_list[i],
indexKeVmaxTest=indexKeVmaxTest_list[i],
indexAngleTolerance=indexAngleTolerance_list[i],
indexH=int(current_indexHKL[0]),
indexK=int(current_indexHKL[1]),
indexL=int(current_indexHKL[2]),
indexH=int(hkl_values[0]),
indexK=int(hkl_values[1]),
indexL=int(hkl_values[2]),
indexCone=indexCone_list[i],
energyUnit=energyUnit_list[i],
exposureUnit=exposureUnit_list[i],
Expand Down Expand Up @@ -1440,9 +1498,9 @@ def submit_parameters(n,
"indexKeVmaxTest": indexKeVmaxTest_list[i],
"indexAngleTolerance": indexAngleTolerance_list[i],
"indexCone": indexCone_list[i],
"indexH": int(current_indexHKL[0]),
"indexK": int(current_indexHKL[1]),
"indexL": int(current_indexHKL[2]),
"indexH": int(hkl_values[0]),
"indexK": int(hkl_values[1]),
"indexL": int(hkl_values[2]),
})

session.commit()
Expand Down
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