diff --git a/__pycache__/download_gedi.cpython-312.pyc b/__pycache__/download_gedi.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..348b574424d303ca67090b88f746483009ea50be Binary files /dev/null and b/__pycache__/download_gedi.cpython-312.pyc differ diff --git a/__pycache__/get_gedi_data.cpython-312.pyc b/__pycache__/get_gedi_data.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..fde21e3b2669504f0372e45cd2a8817f1f243326 Binary files /dev/null and b/__pycache__/get_gedi_data.cpython-312.pyc differ diff --git a/__pycache__/pgap.cpython-312.pyc b/__pycache__/pgap.cpython-312.pyc new file mode 100644 index 0000000000000000000000000000000000000000..a0c351388cda50c1b4ddca5687c855ddc7fadde7 Binary files /dev/null and b/__pycache__/pgap.cpython-312.pyc differ diff --git a/get_gedi_data.py b/get_gedi_data.py index fd77e7e07591b67aa4f3205334c88d42ad8a10c7..4ab61b4ae2d2f9c2d49fa1d2f9845c49619f905b 100644 --- a/get_gedi_data.py +++ b/get_gedi_data.py @@ -1,4 +1,4 @@ -1import sys +import sys import h5py import boto3 import botocore @@ -21,7 +21,8 @@ def get_gedi_data(url): secret=credentials['secretAccessKey'], token=credentials['sessionToken'] ) - with s3.open(lpdaac_gedi_https_to_s3(url), "rb") as f: - gedi_ds = h5py.File(f, "r") - + # with s3.open(lpdaac_gedi_https_to_s3(url), "rb") as f: + # gedi_ds = h5py.File(f, "r") + # return gedi_ds + gedi_ds = h5py.File(s3.open(lpdaac_gedi_https_to_s3(url), "rb"), "r") return gedi_ds \ No newline at end of file diff --git a/main.py b/main.py index 025e500c4f4325295070f4bf1c3e72d0942aa2cf..08bc00d997c0eec5a289c9b6b00778002010f2d8 100644 --- a/main.py +++ b/main.py @@ -69,13 +69,11 @@ def gedi_bioindex(index,l1b_ds,l2a_ds, beam, beam_filt, allom_df): # get bioindex using HSE from NEON db analysis beam_domain = beam_filt.loc[index]['DomainID'] - print(beam_domain) try: if pd.isnull(beam_domain): cval = 1.63 else: cval = allom_df[allom_df['domain']==beam_domain]['HSE'].values[0] - print(cval) # get pgap pgap = GapDS(waveform_smooth, ht_arr, np.array([rh100]), calc_refl_vg = False, utm_x=None,utm_y=None,cval=cval) diff --git a/notebooks/run-gedi-biomass.ipynb b/notebooks/run-gedi-biomass.ipynb index fcfacd9729c45453bcc6cad51bef10672a03891c..29db5f1a530e8dd5155d870caf9a70b2feda762e 100644 --- a/notebooks/run-gedi-biomass.ipynb +++ b/notebooks/run-gedi-biomass.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 7, + "execution_count": 1, "id": "25172537-794b-4135-bb28-63c0fcefbb68", "metadata": {}, "outputs": [ @@ -27,7 +27,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 2, "id": "f176e75b-5104-478b-ade6-a84006e966b0", "metadata": {}, "outputs": [], @@ -48,23 +48,12 @@ "execution_count": 4, "id": "b0d65f96-5dad-44e9-ae85-9d4086c4b29f", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "'https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2022.08.31/GEDI02_A_2022243125140_O21055_03_T02667_02_003_02_V002.h5'" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "b39e76ac-d765-4b8c-baf1-fe41f3296de9", "metadata": {}, "outputs": [ @@ -72,7 +61,18 @@ "name": "stdout", "output_type": "stream", "text": [ - "on file num: 30\r" + "on file num: 200\r" + ] + }, + { + "ename": "KeyboardInterrupt", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[3], line 35\u001b[0m\n\u001b[1;32m 33\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m counter\u001b[38;5;241m%\u001b[39m\u001b[38;5;241m100\u001b[39m\u001b[38;5;241m==\u001b[39m\u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 34\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mon file num: \u001b[39m\u001b[38;5;124m\"\u001b[39m, counter, end\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;130;01m\\r\u001b[39;00m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m---> 35\u001b[0m \u001b[43mtime\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msleep\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m600\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 36\u001b[0m counter\u001b[38;5;241m+\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m\n", + "\u001b[0;31mKeyboardInterrupt\u001b[0m: " ] } ], @@ -109,7 +109,7 @@ " L2A_URL=l2a_fp)\n", " jobs_list.append(job)\n", " \n", - " if counter%10==0:\n", + " if counter%100==0:\n", " print(\"on file num: \", counter, end='\\r')\n", " time.sleep(600)\n", " counter+=1"