60 lines
14 KiB
Plaintext
60 lines
14 KiB
Plaintext
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‡ààhº$ ã óT — d Z ddlmZ ddlmZ ddlmZmZmZmZ ddl Z
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G d„ d« Z y)zÃ
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Context Generator Service
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This service processes all data files and generates context dictionaries for each page
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of the medical report. It performs analysis on Pnoe, Spirometry, and SECA data.
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é )Údatetime)ÚPath)ÚDictÚListÚOptionalÚTupleNc óÖ — e Zd ZdZd„ Zdededefd„Zd„ Zded efd
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e dej d efd„Zdedeeef d ee fd„Zy)ÚContextGeneratorz&Generate context data for report pagesc ó< — d | _ d | _ d | _ i | _ y )N)Úpnoe_dfÚ
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spirometry_dfÚseca_dfÚ patient_info)Úselfs ú!app/services/context_generator.pyÚ__init__zContextGenerator.__init__ s € ؈Œ Ø !ˆÔ؈Œ Ø ˆÕó Ú pnoe_pathÚspirometry_pathÚ seca_pathc óÄ — t j |d¬« | _ t j |« | _ t j |« | _ | j
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« y)zLoad all required datasetsú;)Ú delimiterN)ÚpdÚread_csvr r
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read_excelr Ú_preprocess_pnoe_data)r r r r s r Ú load_datazContextGenerator.load_data sC € ô —{‘{ 9¸Ô<ˆŒ Ü Ÿ[™[¨ Ó 9ˆÔÜ—}‘} YÓ/ˆŒ Ø ×"Ñ"Õ$r c ó˜ — | j j t j d¬« | _ | j d | j d z | j d< | j d | j d z | j d< | j d | j d z d
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< d}g d¢}|D ]Y }|| j j v sŒ | j | j |d¬« j
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« | j |› d�< Œ[ y)z&Apply preprocessing steps to Pnoe dataÚignore)Úerrorsú VO2(ml/min)úHR(bpm)ú VO2 PulseúBF(bpm)ú
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VO2 Breathz EE(kcal/min)zCARBS(%)éd ÚCHOzFAT(%)ÚFATé
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)
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r" z VCO2(ml/min)r# zVT(l)r% z VE(l/min)r$ r& r( r) é )ÚwindowÚ min_periodsÚ _smoothedN)r Úapplyr Ú
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to_numericÚcolumnsÚrollingÚmean)r Ú window_sizeÚcolumns_to_smoothÚcols r r z&ContextGenerator._preprocess_pnoe_data$ s, € à—|‘|×)Ñ)¬"¯-©-ÀÐ)ÓIˆŒ Ø$(§L¡L° Ñ$?À$Ç,Á,ÈyÑBYÑ$Yˆ� ‰ �[Ñ!Ø%)§\¡\°-Ñ%@À4Ç<Á<ÐPYÑCZÑ%Zˆ� ‰ �\Ñ"Ø "Ÿl™l¨>Ñ :¸T¿\¹\È*Ñ=UÑ UÐX[Ñ [ˆ� ‰ �UÑØ "Ÿl™l¨>Ñ :¸T¿\¹\È(Ñ=SÑ SÐVYÑ Yˆ� ‰ �UÑàˆ ò QÐà$ò vˆCØ�d—l‘l×*Ñ*Ò*Ø26·,±,¸sÑ2C×2KÑ2KÐS^ÐlmÐ2KÓ2n×2sÑ2sÓ2u�— ‘ ˜u IÐ .Ò/ñ vr Ú patient_nameÚreturnc
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ó® — | j ��=| j | j d j j |dd¬« }|j sù|j d }t |j
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| _ | j S )z-Extract patient information from SECA datasetÚLastNameF)ÚcaseÚnar ÚWeightÚ Adult_FMPÚ FirstNameÚ ú ÚAgeÚHeightÚGenderr' g3܀ϣ@r+ )
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ÚnameÚ
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first_nameÚ last_nameÚageÚheightÚweightÚgenderÚfat_percentageÚ fat_mass_lbsÚ
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lean_mass_lbs)
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r ÚstrÚcontainsÚemptyÚilocÚfloatÚgetÚintÚlowerr )r r7 Ú patient_dataÚrowÚ weight_kgÚfat_pcts r Úextract_patient_infoz%ContextGenerator.extract_patient_info3 sE € à �<‰<Ñ #Ø Ÿ<™<¨¯ © °ZÑ(@×(DÑ(D×(MÑ(MÈlÐafÐkpÐ(MÓ(qÑrˆLØ ×%Ò%Ø"×'Ñ'¨Ñ*�Ü ! #§'¡'¨(°AÓ"6Ó 7� Ü §¡¨ °QÓ 7Ó8�ð #Ÿw™w {°BÓ 7Ð 8¸¸#¿'¹'À*ÈbÓ:QÐ9RÐ SØ"%§'¡'¨+°rÓ":Ø!$§¡¨°RÓ!8Ü ˜sŸw™w u¨aÓ 0Ó1Ø!$§¡¨°2Ó!6Ð 7Ø 'Ø !Ÿg™g h°Ó 3× 9Ñ 9Ó ;Ø&-Ø$-°Ñ$7¸#Ñ$=ÀÑ$GØ%.°!°gÀ±mÑ2CÑ%DÀwÑ%Nñ %�Ô!ð × Ñ Ð r c ót — i }dD ]° }| j j | j d j j « |k( }|j rŒQ|j « j
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j d ||› d �< Œ² |S ) z$Calculate spirometry-related metrics)ÚFVCÚFEV1z FEV1/FVC%Ú
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Parametersú/Ú_ú%Ú_pctÚBestr Ú_bestz%Pred.Ú_pred)r
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ÚlocrO ÚstriprQ rV ÚreplaceÚvalues)r ÚmetricsÚparamrX Ú param_keys r Ú calculate_spirometry_metricsz-ContextGenerator.calculate_spirometry_metricsJ sÁ € àˆØ1ò GˆEØ×$Ñ$×(Ñ(¨×);Ñ);¸LÑ)I×)MÑ)M×)SÑ)SÓ)UÐY^Ñ)^Ñ_ˆCØ—9“9Ø !ŸK™K›M× 1Ñ 1°#°sÓ ;× CÑ CÀCÈÓ P� Ø/2°6©{×/AÑ/AÀ!Ñ/D�˜9˜+ UÐ+Ñ,Ø/2°8©}×/CÑ/CÀAÑ/F�˜9˜+ UÐ+Ò,ð Gð ˆr c ó — i }| j d j « |d< |d | j d z |d< | j d j « }| j j | }|d |d< |d |d< | j d j « }| j j | }|d |d
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|||« }|j |« |S )z"Calculate all Pnoe-derived metricszVO2(ml/min)_smoothedÚvo2_maxrJ Úvo2_max_per_kgzVT(l)_smoothedÚpeak_vtúHR(bpm)_smoothedÚ
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peak_vt_hrÚ FAT_smoothedÚ
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fat_max_valueÚ
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fat_max_hrÚvt1Úvt2)r Úmaxr Úidxmaxrg Ú_detect_thresholdsÚ_calculate_hr_zonesÚupdate) r rk Ú peak_vt_idxÚ peak_vt_rowÚ fat_max_idxÚ fat_max_rowrx ry Úzoness r Úcalculate_pnoe_metricsz'ContextGenerator.calculate_pnoe_metricsU s# € àˆØ !Ÿ\™\Ð*@Ñ A× EÑ EÓ Gˆ� ÑØ$+¨IÑ$6¸×9JÑ9JÈ8Ñ9TÑ$TˆÐ Ñ!à—l‘lÐ#3Ñ4×;Ñ;Ó=ˆ Ø—l‘l×&Ñ& {Ñ3ˆ Ø (Ð)9Ñ :ˆ� ÑØ +Ð,>Ñ ?ˆ� Ñ à—l‘l >Ñ2×9Ñ9Ó;ˆ Ø—l‘l×&Ñ& {Ñ3ˆ Ø#.¨~Ñ#>ˆ�Ñ Ø +Ð,>Ñ ?ˆ� Ñ à×*Ñ*Ó,‰ˆˆSØ ˆ�‰Ø ˆ�‰à×(Ñ(¨¨c°;Ó?ˆØ�‰�uÔ Øˆr c óØ — | j d | j d kD }|| j }d}t |« dkD r-|d }| j j | }|d |d |d dœ}| j d j « }|j « }|j « }d} t
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