API Module icescopy temperature import

API Module: icescopy_temperature_import

Temperature import, parsing, reconciliation, and cycle-detection helpers.

Source

• File: src/icescopy_temperature_import.py

Classes

Class	Purpose	Page
TemperatureImportError	Temperature Import Error class.	TemperatureImportError
CSUISDatRow	CSUISDat Row class.	CSUISDatRow
TAMULinkamTimeseries	TAMULinkam Timeseries class.	TAMULinkamTimeseries
StandardTemperatureTimeseries	Standard Temperature Timeseries class.	StandardTemperatureTimeseries
ResolvedImageTimestamps	Resolved Image Timestamps class.	ResolvedImageTimestamps

Module Variables

Variable	Line	Explanation
CSU_IS_TIMESTAMP_RE	15	Stores csu is timestamp re.
TAMU_IMAGE_TIMESTAMP_RE	16	Stores tamu image timestamp re.
TAMU_LDF_TIMESTAMP_RE	21	Stores tamu ldf timestamp re.
GENERIC_FILENAME_TIMESTAMP_RE	25	Stores generic filename timestamp re.
COMPACT_FILENAME_TIMESTAMP_RE	30	Stores compact filename timestamp re.
XLSX_NS	34	Stores xlsx ns.
COMMON_DATETIME_FORMATS	38	Stores common datetime formats.
YEAR4_DASH_DATETIME_FORMATS	52	Stores year4 dash datetime formats.
YEAR4_T_DATETIME_FORMATS	57	Stores year4 t datetime formats.
YEAR4_SLASH_DATETIME_FORMATS	62	Stores year4 slash datetime formats.
YEAR4_COMPACT_DATETIME_FORMATS	67	Stores year4 compact datetime formats.
YEAR2_COMPACT_DATETIME_FORMATS	73	Stores year2 compact datetime formats.
YEAR2_SLASH_DATETIME_FORMATS	85	Stores year2 slash datetime formats.
SLASH_DAY_MONTH_DATETIME_FORMATS	90	Stores slash day month datetime formats.
EXIF_DATETIME_FORMATS	104	Stores exif datetime formats.
INLINE_EXIF_TIMESTAMP_RE	108	Stores inline exif timestamp re.
EPOCH_TIMESTAMP_RE	111	Stores epoch timestamp re.
TIMESTAMP_STYLE_AUTO	113	Stores timestamp style auto.
TIMESTAMP_STYLE_COMMON	114	Stores timestamp style common.
TIMESTAMP_STYLE_YEAR4_DASH	115	Stores timestamp style year4 dash.
TIMESTAMP_STYLE_YEAR4_T	116	Stores timestamp style year4 t.
TIMESTAMP_STYLE_YEAR4_SLASH	117	Stores timestamp style year4 slash.
TIMESTAMP_STYLE_YEAR4_COMPACT	118	Stores timestamp style year4 compact.
TIMESTAMP_STYLE_YEAR2_COMPACT	119	Stores timestamp style year2 compact.
TIMESTAMP_STYLE_YEAR2_SLASH	120	Stores timestamp style year2 slash.
TIMESTAMP_STYLE_EXIF	121	Stores timestamp style exif.
TIMESTAMP_STYLE_EPOCH_SECONDS	122	Stores timestamp style epoch seconds.
TIMESTAMP_STYLE_EPOCH_MILLISECONDS	123	Stores timestamp style epoch milliseconds.
IMAGE_TIMESTAMP_SOURCE_FILENAME	125	Stores image timestamp source filename.
IMAGE_TIMESTAMP_SOURCE_EXIF	126	Stores image timestamp source exif.
IMAGE_TIMESTAMP_SOURCE_CREATED	127	Stores image timestamp source created.
IMAGE_TIMESTAMP_SOURCE_MODIFIED	128	Stores image timestamp source modified.
IMAGE_TIMESTAMP_SOURCE_GENERATED	129	Stores image timestamp source generated.
TEMPERATURE_UNIT_CELSIUS	131	Stores temperature unit celsius.
TEMPERATURE_UNIT_KELVIN	132	Stores temperature unit kelvin.
TIMESTAMP_STYLE_CHOICES	134	Stores timestamp style choices.
IMAGE_TIMESTAMP_SOURCE_CHOICES	147	Stores image timestamp source choices.
TEMPERATURE_UNIT_CHOICES	155	Stores temperature unit choices.

Top-level Functions

Function	Line	Explanation
normalize_sample_name(value)	202	Normalizes sample name.
_parse_csu_is_timestamp(date_text, time_text)	206	Implements parse csu is timestamp.
_safe_int(value, default=0)	223	Implements safe int.
_safe_float(value)	232	Implements safe float.
_normalize_parsed_datetime(value)	239	Implements normalize parsed datetime.
_parse_datetime_with_formats(text, formats)	247	Implements parse datetime with formats.
parse_flexible_datetime_text(text)	256	Parses flexible datetime text.
parse_exif_datetime_text(text)	286	Parses exif datetime text.
parse_year4_dash_datetime_text(text)	293	Parses year4 dash datetime text.
parse_year4_t_datetime_text(text)	300	Parses year4 t datetime text.
parse_year4_slash_datetime_text(text)	307	Parses year4 slash datetime text.
parse_year4_compact_datetime_text(text)	314	Parses year4 compact datetime text.
parse_year2_compact_datetime_text(text)	321	Parses year2 compact datetime text.
parse_year2_slash_datetime_text(text)	328	Parses year2 slash datetime text.
parse_epoch_datetime_text(text, unit='auto')	335	Parses epoch datetime text.
parse_timestamp_text(text, style=TIMESTAMP_STYLE_AUTO)	364	Parses timestamp text.
_datetime_from_filename_match(match)	406	Implements datetime from filename match.
_parse_timestamp_candidates(candidates, style)	425	Implements parse timestamp candidates.
_extract_filename_timestamp_candidates(stem)	433	Implements extract filename timestamp candidates.
parse_generic_image_timestamp(image_name, timestamp_style=TIMESTAMP_STYLE_AUTO)	461	Parses generic image timestamp.
read_exif_timestamp_text(file_path)	469	Reads exif timestamp text.
resolve_image_timestamp(file_path, image_name, source=IMAGE_TIMESTAMP_SOURCE_FILENAME, timestamp_style=TIMESTAMP_STYLE_AUTO, generated_start_text='', frame_interval_seconds=None, image_index=0)	484	Implements resolve image timestamp.
resolve_image_timestamps(image_paths, image_names, source=IMAGE_TIMESTAMP_SOURCE_FILENAME, timestamp_style=TIMESTAMP_STYLE_AUTO, generated_start_text='', frame_interval_seconds=None)	532	Implements resolve image timestamps.
parse_standard_temperature_csv(file_path, timestamp_style=TIMESTAMP_STYLE_AUTO, temperature_unit=TEMPERATURE_UNIT_CELSIUS)	566	Parses standard temperature CSV.
compute_blank_correction_by_index(blank_sample_keys, corrected_counts_by_sample, total_count)	630	Computes blank correction by index.
apply_blank_correction(total_cells, frozen_count, blank_correction)	649	Applies blank correction.
parse_tamu_image_timestamp(image_name)	665	Parses tamu image timestamp.
_read_xlsx_shared_strings(archive)	682	Implements read xlsx shared strings.
_resolve_first_sheet_path(archive)	692	Implements resolve first sheet path.
_read_first_sheet_rows(file_path)	711	Implements read first sheet rows.
_parse_tamu_ldf_timestamp(text)	742	Implements parse tamu ldf timestamp.
_parse_recorded_timestamp(text)	758	Implements parse recorded timestamp.
parse_tamu_linkam_xlsx(file_path)	772	Parses tamu linkam xlsx.
parse_ice_array_calibration_csv(file_path)	842	Parses ice array calibration CSV.
parse_csu_is_dat(file_path)	865	Parses csu is dat.
reconcile_cumulative_counts(raw_counts, anchor_counts, maximum_count)	935	Implements reconcile cumulative counts.
normalize_temperature_reset_threshold(reset_temperature)	988	Normalizes temperature reset threshold.
detect_cycle_start_indexes_from_temperatures(temperatures, reset_temperature, warmup_hysteresis_c=0.02)	997	Detects cycle start indexes from temperatures.
build_cycle_ids_from_start_indexes(total_count, cycle_start_indexes)	1044	Builds cycle ids from start indexes.
reconcile_counts_by_cycle(raw_counts, anchor_counts, maximum_count, cycle_ids)	1069	Implements reconcile counts by cycle.