Gdal: clipping a raster with another raster

I don't know if it's possible to clip a raster with an other raster but you could use gdaltindex to build the shapefile with the extent of your raster.

http://www.gdal.org/gdaltindex.html

For irregular polygons, and assuming that your geotiff raster file is a binary raster, you could use GDAL_Calc:

GDAL_Calc.py -A Mask.tif -B CutBigImageToClip.tif --outfile=SmallerFile.tif --NoDataValue=0 --Calc="B*(A>0)" 

This query will populate 0 where Mask.tif <= 0 and BigImage where the Mask > 0. To do this both rasters must be the same cell size, rows and columns. To extract the same extents use GDAL_Translate with the -projwin ulx uly lrx lry option (box is in projected coordinates), but ensure that the projwin box does not extend over the edges of either raster.

GDAL_Translate -of GTIFF -projwin ulx uly lrx lry BigImageToClip.tif CutBigImageToClip.tif

Substitute values for the projwin box derived from the Mask.

The solution in Python directly, without making shape:

import gdal
from gdalconst import GA_ReadOnly

data = gdal.Open('img_mask.tif', GA_ReadOnly)
geoTransform = data.GetGeoTransform()
minx = geoTransform[0]
maxy = geoTransform[3]
maxx = minx + geoTransform[1] * data.RasterXSize
miny = maxy + geoTransform[5] * data.RasterYSize
call('gdal_translate -projwin ' + ' '.join([str(x) for x in [minx, maxy, maxx, miny]]) + ' -of GTiff img_orig.tif img_out.tif', shell=True)